7TB6 | pdb_00007tb6

Structure of S. maltophilia CapW


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Control of bacterial immune signaling by a WYL domain transcription factor.

Blankenchip, C.L.Nguyen, J.V.Lau, R.K.Ye, Q.Gu, Y.Corbett, K.D.

(2022) Nucleic Acids Res 50: 5239-5250

  • DOI: https://doi.org/10.1093/nar/gkac343
  • Primary Citation Related Structures: 
    7TB5, 7TB6

  • PubMed Abstract: 

    Bacteria use diverse immune systems to defend themselves from ubiquitous viruses termed bacteriophages (phages). Many anti-phage systems function by abortive infection to kill a phage-infected cell, raising the question of how they are regulated to avoid cell killing outside the context of infection. Here, we identify a transcription factor associated with the widespread CBASS bacterial immune system, that we term CapW. CapW forms a homodimer and binds a palindromic DNA sequence in the CBASS promoter region. Two crystal structures of CapW suggest that the protein switches from an unliganded, DNA binding-competent state to a ligand-bound state unable to bind DNA. We show that CapW strongly represses CBASS gene expression in uninfected cells, and that phage infection causes increased CBASS expression in a CapW-dependent manner. Unexpectedly, this CapW-dependent increase in CBASS expression is not required for robust anti-phage activity, suggesting that CapW may mediate CBASS activation and cell death in response to a signal other than phage infection. Our results parallel concurrent reports on the structure and activity of BrxR, a transcription factor associated with the BREX anti-phage system, suggesting that CapW and BrxR are members of a family of universal defense signaling proteins.


  • Organizational Affiliation
    • Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 34.66 kDa 
  • Atom Count: 2,552 
  • Modeled Residue Count: 285 
  • Deposited Residue Count: 299 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
S. maltophilia CapW299Stenotrophomonas maltophiliaMutation(s): 0 
UniProt
Find proteins for A0A8X6EH27 (Stenotrophomonas maltophilia)
Explore A0A8X6EH27 
Go to UniProtKB:  A0A8X6EH27
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8X6EH27
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.033α = 90
b = 113.033β = 90
c = 188.22γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI148814

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references
  • Version 1.2: 2022-06-01
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description