8RW5 | pdb_00008rw5

Symmetry expansion of dimeric transmembrane anti-sigma factor DdvA

• PDB DOI: https://doi.org/10.2210/pdb8RW5/pdb
• EM Map EMD-19543: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Myxococcus xanthus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-02 Released: 2024-11-06 
• Deposition Author(s): Lopez-Alonso, J.P., Ochoa-Lizarralde, B., Tascon, I., Ubarretxena-Belandia, I.
• Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.94 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural basis for regulation of a CBASS-CRISPR-Cas defense island by a transmembrane anti-sigma factor and its ECF sigma partner.

Bernal-Bernal, D., Pantoja-Uceda, D., Lopez-Alonso, J.P., Lopez-Rojo, A., Lopez-Ruiz, J.A., Galbis-Martinez, M., Ochoa-Lizarralde, B., Tascon, I., Elias-Arnanz, M., Ubarretxena-Belandia, I., Padmanabhan, S.

(2024) Sci Adv 10: eadp1053-eadp1053

• PubMed: 39454004 
• DOI: https://doi.org/10.1126/sciadv.adp1053
• Primary Citation Related Structures: 
  8RLZ, 8ROT, 8RW5


• PubMed Abstract: 
  

  How CRISPR-Cas and cyclic oligonucleotide-based antiphage signaling systems (CBASS) are coordinately deployed against invaders remains unclear. We show that a locus containing two CBASS and one type III-B CRISPR-Cas system, regulated by the transmembrane anti-σ DdvA and its cognate extracytoplasmic function (ECF) σ DdvS, can defend Myxococcus xanthus against a phage. Cryo-electron microscopy reveals DdvA-DdvS pairs assemble as arrow-shaped transmembrane dimers. Each DdvA periplasmic domain adopts a separase/craspase-type tetratricopeptide repeat (TPR)-caspase HetF-associated with TPR (TPR-CHAT) architecture with an incomplete His-Cys active site, lacking three α-helices conserved among CHAT domains. Each active site faces the dimer interface, raising the possibility that signal-induced caspase-like DdvA autoproteolysis in trans precedes RseP-mediated intramembrane proteolysis and DdvS release. Nuclear magnetic resonance reveals a DdvA cytoplasmic CHCC-type zinc-bound three-helix bundle that binds to DdvS σ ₂ and σ ₄ domains, undergoing σ ₄ -induced helix extension to trap DdvS. Altogether, we provide structural-mechanistic insights into membrane anti-σ-ECF σ regulation of an antiviral CBASS-CRISPR-Cas defense island.

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Organizational Affiliation: 
• Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQF-CSIC), Universidad de Murcia, 30100 Murcia, Spain.
Instituto de Química Física "Blas Cabrera," CSIC (IQF-CSIC), 28006 Madrid, Spain.
Instituto Biofisika (UPV/EHU, CSIC), 48940 Leioa, Spain.
Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 108.64 kDa 
• Atom Count: 6,753 
• Modeled Residue Count: 872 
• Deposited Residue Count: 991 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHAT domain-containing protein	A [auth B]	991	Myxococcus xanthus	Mutation(s): 0  Gene Names: I5Q59_35855

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.94 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.1
MODEL REFINEMENT	PHENIX	1.21

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Lopez-Alonso, J.P., Ochoa-Lizarralde, B., Tascon, I., Ubarretxena-Belandia, I.

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Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2022-143177NB-I00

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection