Compare revisions

f741a518 · f741a518 · f741a518 · f741a518 · f741a518 · f741a518
--- a/content/3.defense-systems/abiv.md
+++ b/content/3.defense-systems/abiv.md
@@ -10,6 +10,9 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF18728
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1128/AEM.00780-08
 ---

 # AbiV
@@ -34,18 +37,22 @@ The system was detected in 61 different species.
 Proportion of genome encoding the AbiV system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiV
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abiv/AbiV__AbiV-plddts_93.56204.pdb
+dataUrls:
+   - /abiv/AbiV__AbiV.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Haaber_2008[<a href='https://doi.org/10.1128/AEM.00780-08'>Haaber et al., 2008</a>] --> Origin_0
@@ -77,14 +84,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
---
-items:
-    - doi: 10.1023/A:1002027321171
-    - doi: 10.1128/AEM.00780-08
-
---
-::

--- a/content/3.defense-systems/abiz.md
+++ b/content/3.defense-systems/abiz.md
@@ -9,6 +9,9 @@ tableColumns:
    Sensor: Unknown
    Activator: Unknown
    Effector: Membrane disrupting
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1128/JB.00904-06
 ---

 # AbiZ
@@ -33,18 +36,22 @@ The system was detected in 97 different species.
 Proportion of genome encoding the AbiZ system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiZ
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abiz/AbiZ__AbiZ-plddts_78.85683.pdb
+dataUrls:
+   - /abiz/AbiZ__AbiZ.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Durmaz_2007[<a href='https://doi.org/10.1128/JB.00904-06'>Durmaz and  Klaenhammer, 2007</a>] --> Origin_0
@@ -77,13 +84,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts

-::relevant-abstracts
---
-items:
-    - doi: 10.1023/A:1002027321171
-    - doi: 10.1128/JB.00904-06
-
---
-::
--- a/content/3.defense-systems/aditi.md
+++ b/content/3.defense-systems/aditi.md
@@ -10,6 +10,8 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF18928
+relevantAbstracts:
+    - doi: 10.1016/j.chom.2022.09.017
 ---

 # Aditi
@@ -34,25 +36,23 @@ The system was detected in 19 different species.
 Proportion of genome encoding the Aditi system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Aditi
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /aditi/Aditi,Aditi__DitA,0,V-plddts_93.42072.pdb
---
-::
+dataUrls:
+   - /aditi/Aditi.Aditi__DitB.0.V.cif
+   - /aditi/Aditi.Aditi__DitA.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /aditi/Aditi,Aditi__DitB,0,V-plddts_90.75274.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -78,13 +78,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
---
-items:
-    - doi: 10.1016/j.chom.2022.09.017
-
---
-::

--- a/content/3.defense-systems/avs.md
+++ b/content/3.defense-systems/avs.md
@@ -65,24 +65,70 @@ The system was detected in 366 different species.
 Proportion of genome encoding the Avs system for the 14 phyla with more than 50 genomes in the RefSeq database.


+
 ## Structure
+### AVAST_I
+##### Example 1

+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls:
+   - /avs/AVAST_I.AVAST_I__Avs1A.0.V.cif
+   - /avs/AVAST_I.AVAST_I__Avs1C.0.V.cif
+   - /avs/AVAST_I.AVAST_I__Avs1B.0.V.cif

-### Avs_I
+---
+::
+### AVAST_II
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrls: 
-    - /avs/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
-    - /avs/AVAST_I,AVAST_I__Avs1A,0,V-plddts_85.07081.pdb
-    - /avs/AVAST_I,AVAST_I__Avs1C,0,V-plddts_81.74849.pdb
+dataUrls:
+   - /avs/AVAST_II__Avs2A.cif
+
 ---
 ::
+### AVAST_III
+##### Example 1

+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls:
+   - /avs/AVAST_III.AVAST_III__Avs3B.0.V.cif
+   - /avs/AVAST_III.AVAST_III__Avs3A.0.V.cif
+
+---
+::
+### AVAST_IV
+##### Example 1
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls:
+   - /avs/AVAST_IV__Avs4A.cif
+
+---
+::
+### AVAST_V
+##### Example 1
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls:
+   - /avs/AVAST_V__Avs5A.cif
+
+---
+::

 ## Experimental validation

+
 <mermaid>
 graph LR;
    Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
@@ -284,3 +330,4 @@ end
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>

+
--- a/content/3.defense-systems/azaca.md
+++ b/content/3.defense-systems/azaca.md
@@ -10,6 +10,8 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF00271
+relevantAbstracts:
+    - doi: 10.1016/j.chom.2022.09.017
 ---

 # Azaca
@@ -34,32 +36,24 @@ The system was detected in 166 different species.
 Proportion of genome encoding the Azaca system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Azaca
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /azaca/Azaca,Azaca__ZacA,0,V-plddts_85.13072.pdb
---
-::
+dataUrls:
+   - /azaca/Azaca.Azaca__ZacA.0.V.cif
+   - /azaca/Azaca.Azaca__ZacB.0.V.cif
+   - /azaca/Azaca.Azaca__ZacC.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /azaca/Azaca,Azaca__ZacB,0,V-plddts_87.34712.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /azaca/Azaca,Azaca__ZacC,0,V-plddts_86.69875.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -94,13 +88,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
---
-items:
-    - doi: 10.1016/j.chom.2022.09.017
-
---
-::

--- a/content/3.defense-systems/borvo.md
+++ b/content/3.defense-systems/borvo.md
@@ -48,18 +48,22 @@ The system was detected in 79 different species.
 Proportion of genome encoding the Borvo system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Borvo
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /borvo/Borvo__BovA-plddts_90.79263.pdb
+dataUrls:
+   - /borvo/Borvo__BovA.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -87,3 +91,4 @@ end
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>

+
--- a/content/3.defense-systems/brex.md
+++ b/content/3.defense-systems/brex.md
@@ -84,223 +84,81 @@ The system was detected in 888 different species.
 Proportion of genome encoding the BREX system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### BREX_II
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /brex/BREX_II,BREX__brxD,0,DF-plddts_88.40179.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_II,BREX__pglW,0,DF-plddts_77.91126.pdb
---
-::
+dataUrls:
+   - /brex/BREX_VI.BREX__brxHI.0.DF.cif
+   - /brex/BREX_VI.BREX__brxD.0.DF.cif
+   - /brex/BREX_II.BREX__pglY.0.DF.cif
+   - /brex/BREX_II.BREX__pglX2.0.DF.cif
+   - /brex/BREX_II.BREX__pglW.0.DF.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_II,BREX__pglX2,0,DF-plddts_87.98644.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_II,BREX__pglY,0,DF-plddts_83.07386.pdb
 ---
 ::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_II,BREX__pglZ2,0,DF-plddts_86.2672.pdb
---
-::
-
 ### BREX_III
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /brex/BREX_III,BREX__brxA,0,DF-plddts_92.03753.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_III,BREX__brxC,0,DF-plddts_85.62129.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_III,BREX__brxF,0,DF-plddts_95.59973.pdb
---
-::
+dataUrls:
+   - /brex/BREX_III.BREX__brxF.0.DF.cif
+   - /brex/BREX_III.BREX__pglXI.0.DF.cif
+   - /brex/BREX_V.BREX__brxHII.0.DF.cif
+   - /brex/BREX_III.BREX__pglZ3.0.DF.cif
+   - /brex/BREX_III.BREX__brxA.0.DF.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_III,BREX__brxHII,0,DF-plddts_82.85526.pdb
 ---
 ::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_III,BREX__pglXI,0,DF-plddts_86.98487.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_III,BREX__pglZ3,0,DF-plddts_89.03152.pdb
---
-::
-
 ### BREX_IV
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /brex/BREX_IV,BREX__PglZ,0,DF-plddts_86.90171.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_IV,BREX__brxC,0,DF-plddts_85.82022.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_IV,BREX__brxL,0,DF-plddts_92.06923.pdb
---
-::
+dataUrls:
+   - /brex/BREX_IV.BREX__brxP.0.DF.cif
+   - /brex/BREX_IV.BREX__PglZ.0.DF.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_IV,BREX__brxP,0,DF-plddts_88.53431.pdb
 ---
 ::
-
 ### BREX_V
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /brex/BREX_V,BREX__brxA_DUF1819,0,DF-plddts_96.04893.pdb
---
-::
+dataUrls:
+   - /brex/BREX_V.BREX__brxHII.0.DF.cif
+   - /brex/BREX_VI.BREX__pglZA.0.DF.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_V,BREX__brxB_DUF1788,0,DF-plddts_90.45365.pdb
 ---
 ::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_V,BREX__brxC,0,DF-plddts_82.61479.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_V,BREX__brxHII,0,DF-plddts_83.9134.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_V,BREX__pglX1,0,DF-plddts_92.49306.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_V,BREX__pglZA,0,DF-plddts_92.2016.pdb
---
-::
-
 ### BREX_VI
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /brex/BREX_VI,BREX__brxB_DUF1788,0,DF-plddts_91.60152.pdb
---
-::
+dataUrls:
+   - /brex/BREX_VI.BREX__brxHI.0.DF.cif
+   - /brex/BREX_VI.BREX__brxD.0.DF.cif
+   - /brex/BREX_VI.BREX__pglZA.0.DF.cif
+   - /brex/BREX_VI.BREX_brxA.0.DF.cif
+   - /brex/BREX_VI.BREX__brxE.0.DF.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_VI,BREX__brxC,0,DF-plddts_86.1139.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_VI,BREX__brxD,0,DF-plddts_90.67427.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_VI,BREX__brxE,0,DF-plddts_90.30329.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_VI,BREX__brxHI,0,DF-plddts_87.87451.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_VI,BREX__pglX1,0,DF-plddts_78.09923.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_VI,BREX__pglZA,0,DF-plddts_88.59061.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /brex/BREX_VI,BREX_brxA,0,DF-plddts_93.93224.pdb
 ---
 ::

 ## Experimental validation

+
 <mermaid>
 graph LR;
    Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -347,3 +205,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+
--- a/content/3.defense-systems/bsta.md
+++ b/content/3.defense-systems/bsta.md
@@ -9,6 +9,8 @@ tableColumns:
    Sensor: Unknown
    Activator: Unknown
    Effector: Unknown
+relevantAbstracts:
+    - doi: 10.1016/j.chom.2021.09.002
 ---

 # BstA
@@ -43,32 +45,24 @@ The system was detected in 88 different species.
 Proportion of genome encoding the BstA system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### BstA
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /bsta/BstA__BstA-plddts_84.76542.pdb
---
-::
+dataUrls:
+   - /bsta/BstA__BstA.cif
+   - /bsta/BstA__BstA1.cif
+   - /bsta/BstA__BstA2.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /bsta/BstA__BstA1-plddts_85.78689.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /bsta/BstA__BstA2-plddts_92.11235.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Owen_2021[<a href='https://doi.org/10.1016/j.chom.2021.09.002'>Owen et al., 2021</a>] --> Origin_0
@@ -127,17 +121,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
---
-items:
-    - doi: 10.1016/j.chom.2021.09.002
-
---
-::
-
-
-## References

-1. Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe. 2021 Nov 10;29(11):1620-1633.e8. doi: 10.1016/j.chom.2021.09.002. Epub 2021 Sep 30. PMID: 34597593; PMCID: PMC8585504.
--- a/content/3.defense-systems/bunzi.md
+++ b/content/3.defense-systems/bunzi.md
@@ -45,25 +45,23 @@ The system was detected in 58 different species.
 Proportion of genome encoding the Bunzi system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Bunzi
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /bunzi/Bunzi,Bunzi__BnzA,0,V-plddts_83.13475.pdb
---
-::
+dataUrls:
+   - /bunzi/Bunzi.Bunzi__BnzB.0.V.cif
+   - /bunzi/Bunzi.Bunzi__BnzA.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /bunzi/Bunzi,Bunzi__BnzB,0,V-plddts_86.79774.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -89,3 +87,4 @@ end
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>

+
--- a/content/3.defense-systems/butters_gp30_gp31.md
+++ b/content/3.defense-systems/butters_gp30_gp31.md
@@ -57,25 +57,23 @@ The system was detected in 34 different species.
 Proportion of genome encoding the Butters_gp30_gp31 system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Butters_gp30_gp31
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp30-plddts_79.33298.pdb
---
-::
+dataUrls:
+   - /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp30.cif
+   - /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp31.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp31-plddts_84.75463.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Mageeney_2020[<a href='https://doi.org/10.1128/mSystems.00534-20'>Mageeney et al., 2020</a>] --> Origin_0

--- a/content/3.defense-systems/butters_gp57r.md
+++ b/content/3.defense-systems/butters_gp57r.md
@@ -6,6 +6,8 @@ tableColumns:
      doi: 10.1101/2023.01.03.522681
      abstract: |
        During lysogeny temperate phages establish a truce with the bacterial host. In this state, the phage genome (prophage) is maintained within the host environment. Consequently, many prophages have evolved systems to protect the host from heterotypic viral attack. This phenomenon of prophages mediating defense of their host against competitor phages is widespread among temperate mycobacteriophages. We previously showed that the Mycobacterium phage Butters prophage encodes a two-component system (gp30/31) that inhibits infection from a subset of mycobacteriophages that include PurpleHaze, but not Island3. Here we show that Butters gp57r is both necessary and sufficient to inhibit infection by Island3 and other phages. Gp57r acts post-DNA injection and its antagonism results in the impairment of Island3 DNA amplification. Gp57r inhibition of Island3 is absolute with no defense escape mutants. However, mutations mapping to minor tail proteins allow PurpleHaze to overcome gp57r defense. Gp57r has a HEPN domain which is present in many proteins involved in inter-genomic conflicts, suggesting that gp57r may inhibit heterotypic phage infections via its HEPN domain. We also show that Butters gp57r has orthologues in clinical isolates of Mycobacterium abscessus sp. including the phage therapy candidate strain GD91 which was found to be resistant to the panel of phages tested. It is conceivable that this GD91 orthologue of gp57r may mediate resistance to the subset of phages tested. Challenges of this nature underscore the importance of elucidating mechanisms of antiphage systems and mutations that allow for escape from inhibition. IMPORTANCE The evolutionary arms race between phages and their bacteria host is ancient. During lysogeny, temperate phages establish a ceasefire with the host where they do not kill the host but derive shelter from it. Within the phenomenon of prophage-mediated defense, some temperate phages contribute genes that make their host more fit and resistant to infections by other phages. This arrangement has significance for both phage and bacterial evolutionary dynamics. Further, the prevalence of such antiphage systems poses a challenge to phage therapy. Thus, studies aimed at elucidating antiphage systems will further our understanding of phage-bacteria evolution as well as help with efforts to engineer therapeutic phages that circumvent antiphage systems.
+relevantAbstracts:
+    - doi: 10.1101/2023.01.03.522681
 ---

 # Butters_gp57r
@@ -33,18 +35,22 @@ The system was detected in 7 different species.
 Proportion of genome encoding the Butters_gp57r system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Butters_gp57r
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /butters_gp57r/Butters_gp57r__gp57r-plddts_90.7432.pdb
+dataUrls:
+   - /butters_gp57r/Butters_gp57r__gp57r.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Mohammed_2023[<a href='https://doi.org/10.1101/2023.01.03.522681'>Mohammed et al., 2023</a>] --> Origin_0
@@ -75,11 +81,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstract
-::relevant-abstracts
---
-items:
-    - doi: 10.1101/2023.01.03.522681

---
-::
--- a/content/3.defense-systems/caprel.md
+++ b/content/3.defense-systems/caprel.md
@@ -10,6 +10,8 @@ tableColumns:
    Activator: Direct
    Effector: Nucleic acid degrading (pyrophosphorylates tRNAs)
    PFAM: PF04607
+relevantAbstracts:
+    - doi: 10.1038/s41586-022-05444-z
 ---

 # CapRel
@@ -46,18 +48,22 @@ The system was detected in 217 different species.
 Proportion of genome encoding the CapRel system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### CapRel
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /caprel/CapRel__CapRel-plddts_90.09132.pdb
+dataUrls:
+   - /caprel/CapRel__CapRel.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Zhang_2022[<a href='https://doi.org/10.1038/s41586-022-05444-z'>Zhang et al., 2022</a>] --> Origin_0
@@ -99,17 +105,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
---
-items:
-    - doi: 10.1038/s41586-022-05444-z
-
---
-::
-
-
-## References
-Zhang T, Tamman H, Coppieters 't Wallant K, Kurata T, LeRoux M, Srikant S, Brodiazhenko T, Cepauskas A, Talavera A, Martens C, Atkinson GC, Hauryliuk V, Garcia-Pino A, Laub MT. Direct activation of a bacterial innate immune system by a viral capsid protein. Nature. 2022 Dec;612(7938):132-140. doi: 10.1038/s41586-022-05444-z. Epub 2022 Nov 16. PMID: 36385533.

--- a/content/3.defense-systems/cas.md
+++ b/content/3.defense-systems/cas.md
---
-title: CRISPR-Cas
-layout: article
-tableColumns:
-    article:
-      doi: 10.1038/nrmicro3569
-      abstract: |
-        The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
---
-
-# CRISPR-Cas
-
-For the CRISPR-Cas system, a good place to start is the [Wikipedia page](https://en.wikipedia.org/wiki/CRISPR)
-
-## Example of genomic structure
-
-CRISPR-Cas systems have been classified in 6 different families :ref{doi=10.1038/s41579-019-0299-x}.
-Each family is composed of different subtypes. For example, Type I CRISPR is composed of 7 subtypes: I-A to I-G.
-
-Here is example of each of the 6 family found in the RefSeq database:
-
-![cas_class1-subtype-i-e](/cas/CAS_Class1-Subtype-I-E.svg){max-width=750px}
-
-The CAS_Class1-Subtype-I-E system in *Citrobacter sp. RHBSTW-00017* (GCF_013797615.1, NZ_CP056899) is composed of 8 proteins cas3_I_5 (WP_103284157.1) cas8e_I-E_1 (HV037_RS05730) cse2gr11_I-E_2 (HV037_RS05735) cas7_I-E_2 (HV037_RS05740) cas5_I-E_3 (HV037_RS05745) cas6e_I_II_III_IV_V_VI_1 (HV037_RS05750) cas1_I-E_1 (HV037_RS05755) cas2_I-E_2 (HV037_RS05760) 
-
-![cas_class2-subtype-ii-a](/cas/CAS_Class2-Subtype-II-A.svg){max-width=750px}
-
-The CAS_Class2-Subtype-II-A system in *Streptococcus agalactiae* (GCF_001190885.1, NZ_CP011329) is composed of 4 proteins cas9_II-A_II-B_II-C_3 (SAH002_RS04760) cas1_I_II_III_IV_V_VI_5 (SAH002_RS04765) cas2_I_II_III_IV_V_VI_6 (SAH002_RS04770) csn2_II-A_4 (SAH002_RS04775) 
-
-![cas_class1-subtype-iii-a](/cas/CAS_Class1-Subtype-III-A.svg){max-width=750px}
-
-The CAS_Class1-Subtype-III-A system in *Mycobacterium tuberculosis* (GCF_014900005.1, NZ_CP041828) is composed of 9 proteins cas2_I_II_III_IV_V_VI_5 (FPJ80_RS14760) cas1_I_II_III_IV_V_VI_8 (FPJ80_RS14765) csm6_III_2 (FPJ80_RS14770) csm5gr7_III-A_3 (FPJ80_RS14775) csm4gr5_III-A_3 (FPJ80_RS14780) csm3gr7_III-A_1 (FPJ80_RS14785) csm2gr11_III-A_1 (FPJ80_RS14790) cas10_III_7 (FPJ80_RS14795) cas6_I_II_III_IV_V_VI_15 (FPJ80_RS14800) 
-
-![cas_class1-subtype-iv-a](/cas/CAS_Class1-Subtype-IV-A.svg){max-width=750px}
-
-The CAS_Class1-Subtype-IV-A system in *Shigella flexneri* (GCF_022353685.1, NZ_CP054978) is composed of 5 proteins csf1gr8_IV-A_3 (WP_038989757.1) cas6e_I_II_III_IV_V_VI_3 (WP_038989755.1) csf4_IV-A_1 (WP_016947078.1) csf3gr5_IV-A_1 (WP_004181864.1) csf2gr7_IV-A_1 (WP_029505552.1) 
-
-
-![cas_class2-subtype-v-a](/cas/CAS_Class2-Subtype-V-A.svg){max-width=750px}
-
-The CAS_Class2-Subtype-V-A system in *Francisella tularensis* (GCF_001865695.1, NZ_CP016635) is composed of 4 proteins cas2_I_II_III_IV_V_VI_3 (N894_RS07580) cas1_I_II_III_IV_V_VI_1 (N894_RS07585) cas4_V_1 (N894_RS07590) cas12a_V-A_4 (N894_RS07595) 
-
-![cas_class2-subtype-vi-a](/cas/CAS_Class2-Subtype-VI-A.svg){max-width=750px}
-
-The CAS_Class2-Subtype-VI-A system in *Leptotrichia shahii* (GCF_008327825.1, NZ_AP019827) is composed of 3 proteins cas13a_VI-A_1 (F1564_RS00570) cas1_I_II_III_IV_V_VI_5 (F1564_RS00575) cas2_I_II_III_IV_V_VI_11 (F1564_RS00580) 
-
-## Distribution of the system among prokaryotes
-
-Among the 22,803 complete genomes of RefSeq, the AbiC is detected in 8581 genomes (37.63 %).
-
-The system was detected in 2905 different species.
-
-![cas](/cas/Distribution_Cas.svg){max-width=750px}
-
-Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.
+---
+title: CRISPR-Cas
+layout: article
+tableColumns:
+    article:
+      doi: 10.1038/nrmicro3569
+      abstract: |
+        The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
+---
+
+# CRISPR-Cas
+
+For the CRISPR-Cas system, a good place to start is the [Wikipedia page](https://en.wikipedia.org/wiki/CRISPR)
+
+## Example of genomic structure
+
+CRISPR-Cas systems have been classified in 6 different families :ref{doi=10.1038/s41579-019-0299-x}.
+Each family is composed of different subtypes. For example, Type I CRISPR is composed of 7 subtypes: I-A to I-G.
+
+Here is example of each of the 6 family found in the RefSeq database:
+
+![cas_class1-subtype-i-e](/cas/CAS_Class1-Subtype-I-E.svg){max-width=750px}
+
+The CAS_Class1-Subtype-I-E system in *Citrobacter sp. RHBSTW-00017* (GCF_013797615.1, NZ_CP056899) is composed of 8 proteins cas3_I_5 (WP_103284157.1) cas8e_I-E_1 (HV037_RS05730) cse2gr11_I-E_2 (HV037_RS05735) cas7_I-E_2 (HV037_RS05740) cas5_I-E_3 (HV037_RS05745) cas6e_I_II_III_IV_V_VI_1 (HV037_RS05750) cas1_I-E_1 (HV037_RS05755) cas2_I-E_2 (HV037_RS05760) 
+
+![cas_class2-subtype-ii-a](/cas/CAS_Class2-Subtype-II-A.svg){max-width=750px}
+
+The CAS_Class2-Subtype-II-A system in *Streptococcus agalactiae* (GCF_001190885.1, NZ_CP011329) is composed of 4 proteins cas9_II-A_II-B_II-C_3 (SAH002_RS04760) cas1_I_II_III_IV_V_VI_5 (SAH002_RS04765) cas2_I_II_III_IV_V_VI_6 (SAH002_RS04770) csn2_II-A_4 (SAH002_RS04775) 
+
+![cas_class1-subtype-iii-a](/cas/CAS_Class1-Subtype-III-A.svg){max-width=750px}
+
+The CAS_Class1-Subtype-III-A system in *Mycobacterium tuberculosis* (GCF_014900005.1, NZ_CP041828) is composed of 9 proteins cas2_I_II_III_IV_V_VI_5 (FPJ80_RS14760) cas1_I_II_III_IV_V_VI_8 (FPJ80_RS14765) csm6_III_2 (FPJ80_RS14770) csm5gr7_III-A_3 (FPJ80_RS14775) csm4gr5_III-A_3 (FPJ80_RS14780) csm3gr7_III-A_1 (FPJ80_RS14785) csm2gr11_III-A_1 (FPJ80_RS14790) cas10_III_7 (FPJ80_RS14795) cas6_I_II_III_IV_V_VI_15 (FPJ80_RS14800) 
+
+![cas_class1-subtype-iv-a](/cas/CAS_Class1-Subtype-IV-A.svg){max-width=750px}
+
+The CAS_Class1-Subtype-IV-A system in *Shigella flexneri* (GCF_022353685.1, NZ_CP054978) is composed of 5 proteins csf1gr8_IV-A_3 (WP_038989757.1) cas6e_I_II_III_IV_V_VI_3 (WP_038989755.1) csf4_IV-A_1 (WP_016947078.1) csf3gr5_IV-A_1 (WP_004181864.1) csf2gr7_IV-A_1 (WP_029505552.1) 
+
+
+![cas_class2-subtype-v-a](/cas/CAS_Class2-Subtype-V-A.svg){max-width=750px}
+
+The CAS_Class2-Subtype-V-A system in *Francisella tularensis* (GCF_001865695.1, NZ_CP016635) is composed of 4 proteins cas2_I_II_III_IV_V_VI_3 (N894_RS07580) cas1_I_II_III_IV_V_VI_1 (N894_RS07585) cas4_V_1 (N894_RS07590) cas12a_V-A_4 (N894_RS07595) 
+
+![cas_class2-subtype-vi-a](/cas/CAS_Class2-Subtype-VI-A.svg){max-width=750px}
+
+The CAS_Class2-Subtype-VI-A system in *Leptotrichia shahii* (GCF_008327825.1, NZ_AP019827) is composed of 3 proteins cas13a_VI-A_1 (F1564_RS00570) cas1_I_II_III_IV_V_VI_5 (F1564_RS00575) cas2_I_II_III_IV_V_VI_11 (F1564_RS00580) 
+
+## Distribution of the system among prokaryotes
+
+Among the 22,803 complete genomes of RefSeq, the AbiC is detected in 8581 genomes (37.63 %).
+
+The system was detected in 2905 different species.
+
+![cas](/cas/Distribution_Cas.svg){max-width=750px}
+
+Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.
--- a/content/3.defense-systems/cbass.md
+++ b/content/3.defense-systems/cbass.md
@@ -10,6 +10,13 @@ tableColumns:
    Activator: Signaling molecules
    Effector: Divers (Nucleic acid degrading, Nucleotide modifying, Membrane disrupting)
    PFAM: PF00004, PF00027, PF00899, PF01048, PF01734, PF06508, PF10137, PF14461, PF14464, PF18134, PF18138, PF18144, PF18145, PF18153, PF18159, PF18167, PF18173, PF18178, PF18179, PF18186, PF18303, PF18967
+relevantAbstracts:
+    - doi: 10.1016/j.molcel.2019.12.009
+    - doi: 10.1016/j.molcel.2021.10.020
+    - doi: 10.1038/s41564-020-0777-y
+    - doi: 10.1038/s41586-019-1605-5
+    - doi: 10.1038/s41586-020-2719-5
+
 ---

 # CBASS
@@ -46,129 +53,67 @@ The system was detected in 1290 different species.
 Proportion of genome encoding the CBASS system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### CBASS_I
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /cbass/CBASS_I,CBASS__Cyclase_II,0,V-plddts_92.48144.pdb
---
-::
+dataUrls:
+   - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.cif
+   - /cbass/CBASS_I.CBASS__TM.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /cbass/CBASS_I,CBASS__TM,0,V-plddts_91.45177.pdb
 ---
 ::
-
 ### CBASS_II
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /cbass/CBASS_II,CBASS__AG_E2_Prok-E2,0,V-plddts_89.8018.pdb
---
-::
+dataUrls:
+   - /cbass/CBASS_II.CBASS__Phospholipase.0.V.cif
+   - /cbass/CBASS_II.CBASS__AG_E2_Prok-E2.0.V.cif
+   - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.cif
+   - /cbass/CBASS_II.CBASS__Jab.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /cbass/CBASS_II,CBASS__Cyclase_II,0,V-plddts_89.65358.pdb
 ---
 ::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /cbass/CBASS_II,CBASS__Jab,0,V-plddts_95.53434.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /cbass/CBASS_II,CBASS__Phospholipase,0,V-plddts_89.1622.pdb
---
-::
-
 ### CBASS_III
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /cbass/CBASS_III,CBASS__Cyclase_II,0,V-plddts_97.70389.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /cbass/CBASS_III,CBASS__Endonuc_small,0,V-plddts_97.03481.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /cbass/CBASS_III,CBASS__HORMA,0,V-plddts_89.50696.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /cbass/CBASS_III,CBASS__TRIP13,0,V-plddts_89.6492.pdb
---
-::
+dataUrls:
+   - /cbass/CBASS_III.CBASS__Endonuc_small.0.V.cif
+   - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.cif
+   - /cbass/CBASS_III.CBASS__bacHORMA_2.0.V.cif
+   - /cbass/CBASS_III.CBASS__HORMA.0.V.cif
+   - /cbass/CBASS_III.CBASS__TRIP13.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /cbass/CBASS_III,CBASS__bacHORMA_2,0,V-plddts_84.43633.pdb
 ---
 ::
-
 ### CBASS_IV
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /cbass/CBASS_IV,CBASS__2TM_type_IV,0,DF-plddts_87.89742.pdb
---
-::
+dataUrls:
+   - /cbass/CBASS_IV.CBASS__QueC.0.DF.cif
+   - /cbass/CBASS_IV.CBASS__TGT.0.DF.cif
+   - /cbass/CBASS_IV.CBASS__Cyclase_SMODS.0.DF.cif
+   - /cbass/CBASS_IV.CBASS__2TM_type_IV.0.DF.cif
+   - /cbass/CBASS_IV.CBASS__OGG.0.DF.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /cbass/CBASS_IV,CBASS__Cyclase_SMODS,0,DF-plddts_87.98201.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /cbass/CBASS_IV,CBASS__OGG,0,DF-plddts_95.21551.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /cbass/CBASS_IV,CBASS__QueC,0,DF-plddts_93.98141.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /cbass/CBASS_IV,CBASS__TGT,0,DF-plddts_93.84001.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Cohen_2019[<a href='https://doi.org/10.1038/s41586-019-1605-5'>Cohen et al., 2019</a>] --> Origin_0
@@ -225,17 +170,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
---
-items:
-    - doi: 10.1016/j.molcel.2019.12.009
-    - doi: 10.1016/j.molcel.2021.10.020
-    - doi: 10.1038/s41564-020-0777-y
-    - doi: 10.1038/s41586-019-1605-5
-    - doi: 10.1038/s41586-020-2719-5
-
---
-::

--- a/content/3.defense-systems/charlie_gp32.md
+++ b/content/3.defense-systems/charlie_gp32.md
@@ -6,6 +6,8 @@ tableColumns:
      doi: 10.1038/nmicrobiol.2016.251
      abstract: |
        Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+relevantAbstracts:
+    - doi: 10.1038/nmicrobiol.2016.251
 ---

 # Charlie_gp32
@@ -33,18 +35,22 @@ The system was detected in 47 different species.
 Proportion of genome encoding the Charlie_gp32 system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Charlie_gp32
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /charlie_gp32/Charlie_gp32__gp32-plddts_82.99758.pdb
+dataUrls:
+   - /charlie_gp32/Charlie_gp32__gp32.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Dedrick_2017[<a href='https://doi.org/10.1038/nmicrobiol.2016.251'>Dedrick et al., 2017</a>] --> Origin_0
@@ -68,11 +74,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstract
-::relevant-abstracts
---
-items:
-    - doi: 10.1038/nmicrobiol.2016.251

---
-::
--- a/content/3.defense-systems/dartg.md
+++ b/content/3.defense-systems/dartg.md
@@ -50,25 +50,23 @@ The system was detected in 386 different species.
 Proportion of genome encoding the DarTG system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### DarTG
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /dartg/DarTG,DarTG_DarG,0,DF-plddts_94.40611.pdb
---
-::
+dataUrls:
+   - /dartg/DarTG.DarTG_DarT.0.DF.cif
+   - /dartg/DarTG.DarTG_DarG.0.DF.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /dartg/DarTG,DarTG_DarT,0,DF-plddts_94.62475.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Leroux_2022[<a href='https://doi.org/10.1038/s41564-022-01153-5'>LeRoux et al., 2022</a>] --> Origin_0
@@ -96,3 +94,4 @@ end
 </mermaid>
 ::

+
--- a/content/3.defense-systems/dazbog.md
+++ b/content/3.defense-systems/dazbog.md
@@ -45,41 +45,34 @@ The system was detected in 50 different species.
 Proportion of genome encoding the Dazbog system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Dazbog
+##### Example 1

-Example 1:
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /dazbog/Dazbog,Dazbog__DzbA,0,V-plddts_87.87307.pdb
---
-::
+dataUrls:
+   - /dazbog/Dazbog.Dazbog__DzbA.1.V.cif
+   - /dazbog/Dazbog.Dazbog__DzbB.1.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /dazbog/Dazbog,Dazbog__DzbB,0,V-plddts_93.82789.pdb
 ---
 ::
+##### Example 2

-Example 2:
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /dazbog/Dazbog,Dazbog__DzbA,0,V-plddts_87.87307.pdb
---
-::
+dataUrls:
+   - /dazbog/Dazbog.Dazbog__DzbA.1.V.cif
+   - /dazbog/Dazbog.Dazbog__DzbB.1.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /dazbog/Dazbog,Dazbog__DzbB,0,V-plddts_93.82789.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -117,3 +110,4 @@ end
 </mermaid>


+
--- a/content/3.defense-systems/dctpdeaminase.md
+++ b/content/3.defense-systems/dctpdeaminase.md
@@ -50,18 +50,22 @@ The system was detected in 294 different species.
 Proportion of genome encoding the dCTPdeaminase system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### dCTPdeaminase
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /dctpdeaminase/dCTPdeaminase__dCTPdeaminase-plddts_91.37723.pdb
+dataUrls:
+   - /dctpdeaminase/dCTPdeaminase__dCTPdeaminase.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Tal_2022[<a href='https://doi.org/10.1038/s41564-022-01158-0'>Tal et al., 2022</a>] --> Origin_0
@@ -134,3 +138,4 @@ end
 </mermaid>


+
--- a/content/3.defense-systems/ddmde.md
+++ b/content/3.defense-systems/ddmde.md
@@ -6,6 +6,8 @@ tableColumns:
      doi: 10.1038/s41586-022-04546-y
      abstract: |
        Horizontal gene transfer can trigger rapid shifts in bacterial evolution. Driven by a variety of mobile genetic elements—in particular bacteriophages and plasmids—the ability to share genes within and across species underpins the exceptional adaptability of bacteria. Nevertheless, invasive mobile genetic elements can also present grave risks to the host; bacteria have therefore evolved a vast array of defences against these elements1. Here we identify two plasmid defence systems conserved in the Vibrio cholerae El Tor strains responsible for the ongoing seventh cholera pandemic2-4. These systems, termed DdmABC and DdmDE, are encoded on two major pathogenicity islands that are a hallmark of current pandemic strains. We show that the modules cooperate to rapidly eliminate small multicopy plasmids by degradation. Moreover, the DdmABC system is widespread and can defend against bacteriophage infection by triggering cell suicide (abortive infection, or Abi). Notably, we go on to show that, through an Abi-like mechanism, DdmABC increases the burden of large low-copy-number conjugative plasmids, including a broad-host IncC multidrug resistance plasmid, which creates a fitness disadvantage that counterselects against plasmid-carrying cells. Our results answer the long-standing question of why plasmids, although abundant in environmental strains, are rare in pandemic strains; have implications for understanding the dissemination of antibiotic resistance plasmids; and provide insights into how the interplay between two defence systems has shaped the evolution of the most successful lineage of pandemic V. cholerae.
+relevantAbstracts:
+    - doi: 10.1038/s41586-022-04546-y
 ---

 # DdmDE
@@ -30,30 +32,17 @@ The system was detected in 50 different species.
 Proportion of genome encoding the DdmDE system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### DdmDE
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /dmdde/DdmDE,DdmDE__DdmD,0,V-plddts_86.22213.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /dmdde/DdmDE,DdmDE__DdmE,0,V-plddts_90.70804.pdb
---
-::
-
-## Relevant abstracts
-
-::relevant-abstracts
---
-items:
-    - doi: 10.1038/s41586-022-04546-y
+dataUrls:
+   - /ddmde/DdmDE.DdmDE__DdmD.0.V.cif
+   - /ddmde/DdmDE.DdmDE__DdmE.0.V.cif

 ---
 ::
--- a/content/3.defense-systems/detocs.md
+++ b/content/3.defense-systems/detocs.md
@@ -65,55 +65,37 @@ The system was detected in 128 different species.
 Proportion of genome encoding the Detocs system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Detocs
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /detocs/Detocs__dtcA-plddts_86.06608.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /detocs/Detocs__dtcB-plddts_95.55971.pdb
---
-::
+dataUrls:
+   - /detocs/Detocs__dtcC.cif
+   - /detocs/Detocs__dtcB.cif
+   - /detocs/Detocs__dtcA.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /detocs/Detocs__dtcC-plddts_94.54261.pdb
 ---
 ::
-
 ### Detocs_hydrolase
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /detocs/Detocs_hydrolase__dtcA-plddts_85.48132.pdb
---
-::
+dataUrls:
+   - /detocs/Detocs_hydrolase__dtcC.cif
+   - /detocs/Detocs_hydrolase__dtcB.cif
+   - /detocs/Detocs_hydrolase__dtcA.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /detocs/Detocs_hydrolase__dtcB-plddts_93.6662.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /detocs/Detocs_hydrolase__dtcC-plddts_89.47253.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Rousset_2023[<a href='https://doi.org/10.1016/j.cell.2023.07.020'>Rousset et al., 2023</a>] --> Origin_0
@@ -156,10 +138,6 @@ end
    style Title2 fill:none,stroke:none,stroke-width:none
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
-<<<<<<< content/3.defense-systems/detocs.md
 </mermaid>


-=======
-</mermaid>
->>>>>>> content/3.defense-systems/detocs.md
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