content/3.defense-systems/gao_mza.md

@@ -45,46 +45,26 @@ The system was detected in 32 different species.
 Proportion of genome encoding the Gao_Mza system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Gao_Mza
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /gao_mza/Gao_Mza,Gao_Mza__MzaA,0,V-plddts_73.82237.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_mza/Gao_Mza,Gao_Mza__MzaB,0,V-plddts_88.82333.pdb
----
-::
+dataUrls:
+   - /gao_mza/Gao_Mza.Gao_Mza__MzaE.0.V.cif
+   - /gao_mza/Gao_Mza.Gao_Mza__MzaD.0.V.cif
+   - /gao_mza/Gao_Mza.Gao_Mza__MzaC.0.V.cif
+   - /gao_mza/Gao_Mza.Gao_Mza__MzaB.0.V.cif
+   - /gao_mza/Gao_Mza.Gao_Mza__MzaA.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_mza/Gao_Mza,Gao_Mza__MzaC,0,V-plddts_83.55691.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_mza/Gao_Mza,Gao_Mza__MzaD,0,V-plddts_88.07953.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_mza/Gao_Mza,Gao_Mza__MzaE,0,V-plddts_87.92462.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -115,3 +95,4 @@ end
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
 
+

content/3.defense-systems/gao_ppl.md

@@ -9,6 +9,8 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+relevantAbstracts:
+    - doi: 10.1126/science.aba0372
 ---
 
 # Gao_Ppl
@@ -33,18 +35,22 @@ The system was detected in 104 different species.
 Proportion of genome encoding the Gao_Ppl system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Gao_Ppl
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /gao_ppl/Gao_Ppl__PplA-plddts_89.89639.pdb
+dataUrls:
+   - /gao_ppl/Gao_Ppl__PplA.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -71,12 +77,4 @@ 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: 10.1126/science.aba0372
-
----
-::

content/3.defense-systems/gao_qat.md

@@ -10,6 +10,8 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF01026, PF07693
+relevantAbstracts:
+    - doi: 10.1126/science.aba0372
 ---
 
 # Gao_Qat
@@ -34,39 +36,25 @@ The system was detected in 267 different species.
 Proportion of genome encoding the Gao_Qat system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Gao_Qat
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /gao_qat/Gao_Qat,Gao_Qat__QatA,0,V-plddts_81.28827.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_qat/Gao_Qat,Gao_Qat__QatB,0,V-plddts_86.3728.pdb
----
-::
+dataUrls:
+   - /gao_qat/Gao_Qat.Gao_Qat__QatA.0.V.cif
+   - /gao_qat/Gao_Qat.Gao_Qat__QatB.0.V.cif
+   - /gao_qat/Gao_Qat.Gao_Qat__QatC.0.V.cif
+   - /gao_qat/Gao_Qat.Gao_Qat__QatD.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_qat/Gao_Qat,Gao_Qat__QatC,0,V-plddts_93.16811.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_qat/Gao_Qat,Gao_Qat__QatD,0,V-plddts_94.78681.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -92,13 +80,4 @@ 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: 10.1126/science.aba0372
-
----
-::
 

content/3.defense-systems/gao_rl.md

@@ -47,39 +47,25 @@ The system was detected in 74 different species.
 Proportion of genome encoding the Gao_RL system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Gao_RL
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /gao_rl/Gao_RL,Gao_RL__RL_A,0,V-plddts_87.81206.pdb
----
-::
+dataUrls:
+   - /gao_rl/Gao_RL.Gao_RL__RL_A.0.V.cif
+   - /gao_rl/Gao_RL.Gao_RL__RL_D.0.V.cif
+   - /gao_rl/Gao_RL.Gao_RL__RL_B.0.V.cif
+   - /gao_rl/Gao_RL.Gao_RL__RL_C.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_rl/Gao_RL,Gao_RL__RL_B,0,V-plddts_87.72993.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_rl/Gao_RL,Gao_RL__RL_C,0,V-plddts_90.086.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_rl/Gao_RL,Gao_RL__RL_D,0,V-plddts_85.47115.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -106,3 +92,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+

content/3.defense-systems/gao_tery.md

@@ -9,6 +9,8 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+relevantAbstracts:
+    - doi: 10.1126/science.aba0372
 ---
 
 # Gao_TerY
@@ -33,32 +35,24 @@ The system was detected in 74 different species.
 Proportion of genome encoding the Gao_TerY system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Gao_TerY
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /gao_tery/Gao_TerY,Gao_TerY__TerYA,0,V-plddts_91.43497.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_tery/Gao_TerY,Gao_TerY__TerYB,0,V-plddts_95.75285.pdb
----
-::
+dataUrls:
+   - /gao_tery/Gao_TerY.Gao_TerY__TerYA.0.V.cif
+   - /gao_tery/Gao_TerY.Gao_TerY__TerYB.0.V.cif
+   - /gao_tery/Gao_TerY.Gao_TerY__TerYC.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_tery/Gao_TerY,Gao_TerY__TerYC,0,V-plddts_81.328.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -85,12 +79,4 @@ 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: 10.1126/science.aba0372
-
----
-::

content/3.defense-systems/gao_tmn.md

@@ -46,18 +46,22 @@ The system was detected in 84 different species.
 Proportion of genome encoding the Gao_Tmn system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Gao_Tmn
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /gao_tmn/Gao_Tmn__TmnA-plddts_82.0142.pdb
+dataUrls:
+   - /gao_tmn/Gao_Tmn__TmnA.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -84,3 +88,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+

content/3.defense-systems/gao_upx.md

@@ -41,18 +41,22 @@ The system was detected in 33 different species.
 Proportion of genome encoding the Gao_Upx system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Gao_Upx
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /gao_upx/Gao_Upx__UpxA-plddts_90.66658.pdb
+dataUrls:
+   - /gao_upx/Gao_Upx__UpxA.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -77,3 +81,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+

content/3.defense-systems/gaps1.md

@@ -45,18 +45,22 @@ The system was detected in 56 different species.
 Proportion of genome encoding the GAPS1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### GAPS1
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /gaps1/GAPS1__GAPS1-plddts_91.57482.pdb
+dataUrls:
+   - /gaps1/GAPS1__GAPS1.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0
@@ -82,3 +86,4 @@ end
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
 
+

content/3.defense-systems/gaps2.md

@@ -7,6 +7,8 @@ tableColumns:
       abstract: |
         Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
     PFAM: PF00533, PF01653, PF03119, PF03120, PF12826, PF14520
+relevantAbstracts:
+    - doi: 10.1101/2023.03.28.534373
 ---
 
 # GAPS2
@@ -34,18 +36,22 @@ The system was detected in 208 different species.
 Proportion of genome encoding the GAPS2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### GAPS2
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /gaps2/GAPS2__GAPS2-plddts_87.94657.pdb
+dataUrls:
+   - /gaps2/GAPS2__GAPS2.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0
@@ -70,12 +76,4 @@ 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: 10.1101/2023.03.28.534373
-
----
-::
 

content/3.defense-systems/gaps4.md

@@ -6,6 +6,8 @@ tableColumns:
       doi: 10.1101/2023.03.28.534373
       abstract: |
         Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+relevantAbstracts:
+    - doi: 10.1101/2023.03.28.534373
 ---
 
 # GAPS4
@@ -33,25 +35,23 @@ The system was detected in 74 different species.
 Proportion of genome encoding the GAPS4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### GAPS4
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /gaps4/GAPS4__GAPS4a-plddts_91.74015.pdb
----
-::
+dataUrls:
+   - /gaps4/GAPS4__GAPS4a.cif
+   - /gaps4/GAPS4__GAPS4b.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gaps4/GAPS4__GAPS4b-plddts_86.45931.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0
@@ -78,11 +78,4 @@ 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: 10.1101/2023.03.28.534373
 
----
-::

content/3.defense-systems/gaps6.md

@@ -6,6 +6,8 @@ tableColumns:
       doi: 10.1101/2023.03.28.534373
       abstract: |
         Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of defense islands may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+relevantAbstracts:
+    - doi: 10.1101/2023.03.28.534373
 ---
 
 # GAPS6
@@ -33,25 +35,23 @@ The system was detected in 33 different species.
 Proportion of genome encoding the GAPS6 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### GAPS6
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /gaps6/GAPS6__GAPS6a-plddts_82.29413.pdb
----
-::
+dataUrls:
+   - /gaps6/GAPS6__GAPS6a.cif
+   - /gaps6/GAPS6__GAPS6b.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gaps6/GAPS6__GAPS6b-plddts_90.04892.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0
@@ -78,11 +78,4 @@ 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: 10.1101/2023.03.28.534373
 
----
-::

content/3.defense-systems/gasdermin.md

@@ -12,8 +12,8 @@ tableColumns:
 contributors: 
   - Aude Bernheim
 relevantAbstracts:
-- doi: 10.1126/science.abj8432
-- doi: 10.1101/2023.05.28.542683
+    - doi: 10.1126/science.abj8432
+    - doi: 10.1101/2023.05.28.542683
 ---
 
 # GasderMIN
@@ -48,53 +48,27 @@ The system was detected in 26 different species.
 Proportion of genome encoding the GasderMIN system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### GasderMIN
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /gasdermin/GasderMIN__ATPase-plddts_79.44181.pdb
----
-::
+dataUrls:
+   - /gasdermin/GasderMIN__bGSDM.cif
+   - /gasdermin/GasderMIN__Protease1.cif
+   - /gasdermin/GasderMIN__Protease2.cif
+   - /gasdermin/GasderMIN__ATPase.cif
+   - /gasdermin/GasderMIN__Protease.cif
+   - /gasdermin/GasderMIN__bGSDM1.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gasdermin/GasderMIN__Protease-plddts_85.56354.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gasdermin/GasderMIN__Protease1-plddts_86.2054.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gasdermin/GasderMIN__Protease2-plddts_85.10965.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gasdermin/GasderMIN__bGSDM-plddts_83.88977.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gasdermin/GasderMIN__bGSDM1-plddts_65.95252.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Johnson_2022[<a href='https://doi.org/10.1371/journal.pgen.1010065'>Johnson et al., 2022</a>] --> Origin_0
@@ -122,3 +96,4 @@ end
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
 
+

content/3.defense-systems/hachiman.md

@@ -10,6 +10,8 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00270, PF00271, PF04851, PF08878, PF14130
+relevantAbstracts:
+    - doi: 10.1126/science.aar4120
 ---
 
 # Hachiman
@@ -40,27 +42,23 @@ The system was detected in 541 different species.
 Proportion of genome encoding the Hachiman system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Hachiman
+##### Example 1
 
-Example 1:
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /hachiman/Hachiman.Hachiman__HamB.0.V-plddts_88.00493.pdb
----
-::
+dataUrls:
+   - /hachiman/Hachiman.Hachiman__HamB.0.V.cif
+   - /hachiman/Hachiman.Hachiman__HamA.0.V.cif
 
-Example 2:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /hachiman/Hachiman.Hachiman__HamB.0.V-plddts_88.00493.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -101,20 +99,4 @@ 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: 10.1126/science.aar4120
-
----
-::
-
-
-## References
-
-1. Doron S, Melamed S, Ofir G, et al. Systematic discovery of antiphage defense systems in the microbial pangenome. *Science*. 2018;359(6379):eaar4120. doi:10.1126/science.aar4120
-
-2. Payne LJ, Todeschini TC, Wu Y, Perry BJ, Ronson CW, Fineran PC, Nobrega FL, Jackson SA. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Res. 2021 Nov 8;49(19):10868-10878. doi: 10.1093/nar/gkab883. PMID: 34606606; PMCID: PMC8565338.
 

content/3.defense-systems/hna.md

@@ -7,6 +7,8 @@ tableColumns:
       abstract: |
         There is strong selection for the evolution of systems that protect bacterial populations from viral attack. We report a single phage defense protein, Hna, that provides protection against diverse phages in Sinorhizobium meliloti, a nitrogen-fixing alpha-proteobacterium. Homologs of Hna are distributed widely across bacterial lineages, and a homologous protein from Escherichia coli also confers phage defense. Hna contains superfamily II helicase motifs at its N terminus and a nuclease motif at its C terminus, with mutagenesis of these motifs inactivating viral defense. Hna variably impacts phage DNA replication but consistently triggers an abortive infection response in which infected cells carrying the system die but do not release phage progeny. A similar host cell response is triggered in cells containing Hna upon expression of a phage-encoded single-stranded DNA binding protein (SSB), independent of phage infection. Thus, we conclude that Hna limits phage spread by initiating abortive infection in response to a phage protein.
     PFAM: PF00270, PF04851, PF13307
+relevantAbstracts:
+    - doi: 10.1016/j.chom.2023.01.010
 ---
 
 # Hna
@@ -34,18 +36,22 @@ The system was detected in 305 different species.
 Proportion of genome encoding the Hna system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Hna
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /hna/Hna__Hna-plddts_91.2064.pdb
+dataUrls:
+   - /hna/Hna__Hna.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -81,12 +87,4 @@ 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: 10.1016/j.chom.2023.01.010
-
----
-::
 

content/3.defense-systems/isg15-like.md

@@ -9,6 +9,9 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+relevantAbstracts:
+    - doi: 10.1016/j.chom.2022.09.017
+
 ---
 
 # ISG15-like
@@ -33,156 +36,77 @@ The system was detected in 39 different species.
 Proportion of genome encoding the ISG15-like system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### ISG15-like
-
-Example 1:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilA,0,V-plddts_93.65636.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilB,0,V-plddts_95.49136.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilC,0,V-plddts_92.06734.pdb
----
-::
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilD,0,V-plddts_93.10226.pdb
----
-::
+dataUrls:
+   - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.cif
 
-Example 2:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilA,0,V-plddts_93.65636.pdb
 ---
 ::
+##### Example 2
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilB,0,V-plddts_95.49136.pdb
----
-::
+dataUrls:
+   - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilC,0,V-plddts_92.06734.pdb
 ---
 ::
+##### Example 3
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilD,0,V-plddts_93.10226.pdb
----
-::
+dataUrls:
+   - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.cif
 
-Example 3:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilA,0,V-plddts_93.65636.pdb
 ---
 ::
+##### Example 4
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilB,0,V-plddts_95.49136.pdb
----
-::
+dataUrls:
+   - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilC,0,V-plddts_92.06734.pdb
 ---
 ::
+##### Example 5
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilD,0,V-plddts_93.10226.pdb
----
-::
+dataUrls:
+   - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.cif
+   - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.cif
 
-Example 4:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilA,0,V-plddts_93.65636.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilB,0,V-plddts_95.49136.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilC,0,V-plddts_92.06734.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilD,0,V-plddts_93.10226.pdb
----
-::
-
-Example 5:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilA,0,V-plddts_93.65636.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilB,0,V-plddts_95.49136.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilC,0,V-plddts_92.06734.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilD,0,V-plddts_93.10226.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
@@ -264,12 +188,4 @@ 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
-
----
-::

content/3.defense-systems/jukab.md

@@ -7,6 +7,8 @@ tableColumns:
       abstract: |
         Jumbo bacteriophages of the ?KZ-like family are characterized by large genomes (>200 kb) and the remarkable ability to assemble a proteinaceous nucleus-like structure. The nucleus protects the phage genome from canonical DNA-targeting immune systems, such as CRISPR-Cas and restriction-modification. We hypothesized that the failure of common bacterial defenses creates selective pressure for immune systems that target the unique jumbo phage biology. Here, we identify the "jumbo phage killer"(Juk) immune system that is deployed by a clinical isolate of Pseudomonas aeruginosa to resist PhiKZ. Juk immunity rescues the cell by preventing early phage transcription, DNA replication, and nucleus assembly. Phage infection is first sensed by JukA (formerly YaaW), which localizes rapidly to the site of phage infection at the cell pole, triggered by ejected phage factors. The effector protein JukB is recruited by JukA, which is required to enable immunity and the subsequent degradation of the phage DNA. JukA homologs are found in several bacterial phyla and are associated with numerous other putative effectors, many of which provided specific antiPhiKZ activity when expressed in P. aeruginosa. Together, these data reveal a novel strategy for immunity whereby immune factors are recruited to the site of phage protein and DNA ejection to prevent phage progression and save the cell.
     PFAM: PF13099
+relevantAbstracts:
+    - doi: 10.1101/2022.09.17.508391
 ---
 
 # JukAB
@@ -34,25 +36,23 @@ The system was detected in 50 different species.
 Proportion of genome encoding the JukAB system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### JukAB
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /jukab/JukAB__JukA-plddts_77.76916.pdb
----
-::
+dataUrls:
+   - /jukab/JukAB__JukB.cif
+   - /jukab/JukAB__JukA.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /jukab/JukAB__JukB-plddts_67.28863.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Li_2022[<a href='https://doi.org/10.1101/2022.09.17.508391'>Li et al., 2022</a>] --> Origin_0
@@ -76,12 +76,4 @@ 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: 10.1101/2022.09.17.508391
-
----
-::
 

content/3.defense-systems/kiwa.md

@@ -47,25 +47,23 @@ The system was detected in 382 different species.
 Proportion of genome encoding the Kiwa system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Kiwa
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /kiwa/Kiwa,Kiwa__KwaA,0,V-plddts_86.99693.pdb
----
-::
+dataUrls:
+   - /kiwa/Kiwa.Kiwa__KwaB.0.V.cif
+   - /kiwa/Kiwa.Kiwa__KwaA.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /kiwa/Kiwa,Kiwa__KwaB,0,V-plddts_93.65136.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -91,3 +89,4 @@ end
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
 
+

content/3.defense-systems/lamassu-fam.md

@@ -96,239 +96,143 @@ The system was detected in 1220 different species.
 Proportion of genome encoding the Lamassu-Fam system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Lamassu-Amidase
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /lamassu-fam/Lamassu-Amidase,Lamassu-Fam__LmuA_effector_Amidase,0,DF-plddts_93.15132.pdb
----
-::
+dataUrls:
+   - /lamassu-fam/Lamassu-Amidase.Lamassu-Fam__LmuA_effector_Amidase.0.DF.cif
+   - /lamassu-fam/Lamassu-Amidase.Lamassu-Fam__LmuB_SMC_Amidase.0.DF.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Amidase,Lamassu-Fam__LmuB_SMC_Amidase,0,DF-plddts_83.58631.pdb
 ---
 ::
-
 ### Lamassu-Cap4_nuclease
+##### Example 1
 
-Example 1:
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /lamassu-fam/Lamassu-Cap4_nuclease,Lamassu-Fam__LmuA_effector_Cap4_nuclease_II,0,DF-plddts_93.57957.pdb
----
-::
+dataUrls:
+   - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuA_effector_Cap4_nuclease_II.0.DF.cif
+   - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuC_acc_Cap4_nuclease.0.DF.cif
+   - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II.0.DF.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Cap4_nuclease,Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II,0,DF-plddts_90.05853.pdb
 ---
 ::
+##### Example 2
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /lamassu-fam/Lamassu-Cap4_nuclease,Lamassu-Fam__LmuC_acc_Cap4_nuclease,0,DF-plddts_91.47415.pdb
----
-::
+dataUrls:
+   - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuA_effector_Cap4_nuclease.1.DF.cif
+   - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam_undetected_LmuC.1.DF.cif
+   - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuB_SMC_Cap4_nuclease.1.DF.cif
 
-Example 2:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Cap4_nuclease,Lamassu-Fam__LmuA_effector_Cap4_nuclease_II,0,DF-plddts_93.57957.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Cap4_nuclease,Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II,0,DF-plddts_90.05853.pdb
 ---
 ::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Cap4_nuclease,Lamassu-Fam__LmuC_acc_Cap4_nuclease,0,DF-plddts_91.47415.pdb
----
-::
-
 ### Lamassu-FMO
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /lamassu-fam/Lamassu-FMO,Lamassu-Fam__LmuA_effector_FMO,0,DF-plddts_90.83272.pdb
----
-::
+dataUrls:
+   - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuB_SMC_FMO.0.DF.cif
+   - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuC_acc_FMO.0.DF.cif
+   - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuA_effector_FMO.0.DF.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-FMO,Lamassu-Fam__LmuB_SMC_FMO,0,DF-plddts_83.19523.pdb
 ---
 ::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-FMO,Lamassu-Fam__LmuC_acc_FMO,0,DF-plddts_89.32543.pdb
----
-::
-
 ### Lamassu-Fam_Hydrolase_Protease
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Hydrolase_Protease,Lamassu-Fam__LmuA_effector_Hydrolase,0,V-plddts_93.45211.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Hydrolase_Protease,Lamassu-Fam__LmuA_effector_Protease,0,V-plddts_90.19112.pdb
----
-::
+dataUrls:
+   - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuA_effector_Hydrolase.0.V.cif
+   - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuA_effector_Protease.0.V.cif
+   - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuC_acc_hydrolase_protease.0.V.cif
+   - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuB_SMC_Hydrolase_protease.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Hydrolase_Protease,Lamassu-Fam__LmuB_SMC_Hydrolase_protease,0,V-plddts_80.40324.pdb
 ---
 ::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Hydrolase_Protease,Lamassu-Fam__LmuC_acc_hydrolase_protease,0,V-plddts_89.02396.pdb
----
-::
-
 ### Lamassu-Fam_Mrr
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Mrr,Lamassu-Fam__LmuA_effector_Mrr,0,V-plddts_84.76528.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Mrr,Lamassu-Fam__LmuB_SMC_Mrr,0,V-plddts_85.79974.pdb
----
-::
+dataUrls:
+   - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuA_effector_Mrr.0.V.cif
+   - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuC_acc_Mrr.0.V.cif
+   - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuB_SMC_Mrr.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Mrr,Lamassu-Fam__LmuC_acc_Mrr,0,V-plddts_86.75101.pdb
 ---
 ::
-
 ### Lamassu-Fam_PDDEXK
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_PDDEXK,Lamassu-Fam__LmuA_effector_PDDEXK,0,V-plddts_90.62277.pdb
----
-::
+dataUrls:
+   - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuA_effector_PDDEXK.0.V.cif
+   - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuB_SMC_PDDEXK.0.V.cif
+   - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuC_acc_PDDEXK.0.V.cif
+   - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuC_acc_PDDEXK.0.V.cif
+   - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuB_SMC_PDDEXK.0.V.cif
+   - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuA_effector_PDDEXK.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_PDDEXK,Lamassu-Fam__LmuB_SMC_PDDEXK,0,V-plddts_83.57058.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_PDDEXK,Lamassu-Fam__LmuC_acc_PDDEXK,0,V-plddts_93.07571.pdb
 ---
 ::
-
 ### Lamassu-Hypothetical
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /lamassu-fam/Lamassu-Hypothetical,Lamassu-Fam__LmuA_effector_hypothetical,0,DF-plddts_87.29909.pdb
----
-::
+dataUrls:
+   - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuB_SMC_hypothetical.0.DF.cif
+   - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuC_acc_hypothetical.0.DF.cif
+   - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuA_effector_hypothetical.0.DF.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Hypothetical,Lamassu-Fam__LmuB_SMC_hypothetical,0,DF-plddts_90.35013.pdb
 ---
 ::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Hypothetical,Lamassu-Fam__LmuC_acc_hypothetical,0,DF-plddts_90.49821.pdb
----
-::
-
 ### Lamassu-Lipase
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /lamassu-fam/Lamassu-Lipase,Lamassu-Fam__LmuA_effector_Lipase,0,DF-plddts_86.47244.pdb
----
-::
+dataUrls:
+   - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuB_SMC_Lipase.0.DF.cif
+   - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuC_acc_Lipase.0.DF.cif
+   - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuA_effector_Lipase.0.DF.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Lipase,Lamassu-Fam__LmuB_SMC_Lipase,0,DF-plddts_89.07634.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Lipase,Lamassu-Fam__LmuC_acc_Lipase,0,DF-plddts_86.70507.pdb
 ---
 ::
-
 ### Lamassu-Sir2
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /lamassu-fam/Lamassu-Sir2,Lamassu-Fam__LmuA_effector_Sir2,0,DF-plddts_89.3866.pdb
----
-::
+dataUrls:
+   - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuB_SMC_Sir2.0.DF.cif
+   - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuC_acc_Sir2.0.DF.cif
+   - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuA_effector_Sir2.0.DF.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Sir2,Lamassu-Fam__LmuB_SMC_Sir2,0,DF-plddts_86.39095.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Sir2,Lamassu-Fam__LmuC_acc_Sir2,0,DF-plddts_85.94734.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -437,3 +341,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+

content/3.defense-systems/lit.md

@@ -51,18 +51,22 @@ The system was detected in 78 different species.
 Proportion of genome encoding the Lit system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Lit
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /lit/Lit__Lit-plddts_91.19971.pdb
+dataUrls:
+   - /lit/Lit__Lit.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Yu_1994[<a href='https://doi.org/10.1073/pnas.91.2.802'>Yu and  Snyder, 1994</a>] --> Origin_0
@@ -86,3 +90,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+

content/3.defense-systems/mads.md

@@ -7,6 +7,8 @@ tableColumns:
       abstract: |
         The constant arms race between bacteria and their phages has resulted in a large diversity of bacterial defence systems1,2, with many bacteria carrying several systems3,4. In response, phages often carry counter-defence genes5-9. If and how bacterial defence mechanisms interact to protect against phages with counter-defence genes remains unclear. Here, we report the existence of a novel defence system, coined MADS (Methylation Associated Defence System), which is located in a strongly conserved genomic defence hotspot in Pseudomonas aeruginosa and distributed across Gram-positive and Gram-negative bacteria. We find that the natural co-existence of MADS and a Type IE CRISPR-Cas adaptive immune system in the genome of P. aeruginosa SMC4386 provides synergistic levels of protection against phage DMS3, which carries an anti-CRISPR (acr) gene. Previous work has demonstrated that Acr-phages need to cooperate to overcome CRISPR immunity, with a first sacrificial phage causing host immunosuppression to enable successful secondary phage infections10,11. Modelling and experiments show that the co-existence of MADS and CRISPR-Cas provides strong and durable protection against Acr-phages by disrupting their cooperation and limiting the spread of mutants that overcome MADS. These data reveal that combining bacterial defences can robustly neutralise phage with counter-defence genes, even if each defence on its own can be readily by-passed, which is key to understanding how selection acts on defence combinations and their coevolutionary consequences.
     PFAM: PF00069, PF01170, PF02384, PF07714, PF08378, PF12728, PF13304, PF13588
+relevantAbstracts:
+    - doi: 10.1101/2023.03.30.534895
 ---
 
 # MADS
@@ -34,60 +36,28 @@ The system was detected in 63 different species.
 Proportion of genome encoding the MADS system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### MADS
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /mads/MADS__mad1-plddts_82.3118.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mads/MADS__mad2-plddts_87.54253.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mads/MADS__mad3-plddts_93.27207.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mads/MADS__mad4-plddts_92.44061.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mads/MADS__mad5-plddts_93.90587.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mads/MADS__mad7-plddts_91.54141.pdb
----
-::
+dataUrls:
+   - /mads/MADS__mad8.cif
+   - /mads/MADS__mad7.cif
+   - /mads/MADS__mad4.cif
+   - /mads/MADS__mad3.cif
+   - /mads/MADS__mad1.cif
+   - /mads/MADS__mad5.cif
+   - /mads/MADS__mad2.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mads/MADS__mad8-plddts_82.23514.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Maestri_2023[<a href='https://doi.org/10.1101/2023.03.30.534895'>Maestri et al., 2023</a>] --> Origin_0
@@ -114,12 +84,4 @@ 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: 10.1101/2023.03.30.534895
-
----
-::