9NYU | pdb_00009nyu

Crystal structure of KwaB dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.324 (Depositor), 0.326 (DCC) 
  • R-Value Work: 
    0.276 (Depositor), 0.277 (DCC) 
  • R-Value Observed: 
    0.281 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites.

Zhang, Z.Todeschini, T.C.Wu, Y.Kogay, R.Naji, A.Cardenas Rodriguez, J.Mondi, R.Kaganovich, D.Taylor, D.W.Bravo, J.P.K.Teplova, M.Amen, T.Koonin, E.V.Patel, D.J.Nobrega, F.L.

(2025) Cell 188: 5862-5877.e23

  • DOI: https://doi.org/10.1016/j.cell.2025.07.002
  • Primary Citation Related Structures: 
    9MRG, 9MRR, 9MRX, 9MTN, 9NYU, 9O0I

  • PubMed Abstract: 

    Bacteria and archaea deploy diverse antiviral defense systems, many of which remain mechanistically uncharacterized. Here, we characterize Kiwa, a widespread two-component system composed of the transmembrane sensor KwaA and the DNA-binding effector KwaB. Cryogenic electron microscopy (cryo-EM) analysis reveals that KwaA and KwaB assemble into a large, membrane-associated supercomplex. Upon phage binding, KwaA senses infection at the membrane, leading to KwaB binding of ejected phage DNA and inhibition of replication and late transcription, without inducing host cell death. Although KwaB can bind DNA independently, its antiviral activity requires association with KwaA, suggesting spatial or conformational regulation. We show that the phage-encoded DNA-mimic protein Gam directly binds and inhibits KwaB but that co-expression with the Gam-targeted RecBCD system restores protection by Kiwa. Our findings support a model in which Kiwa coordinates membrane-associated detection of phage infection with downstream DNA binding by its effector, forming a spatially coordinated antiviral mechanism.


  • Organizational Affiliation
    • Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Interdisciplinary Life Sciences Graduate Programs, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA.

Macromolecule Content 

  • Total Structure Weight: 72.29 kDa 
  • Atom Count: 5,058 
  • Modeled Residue Count: 626 
  • Deposited Residue Count: 630 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kiwa protein KwaBA,
B [auth K]
315Escherichia coliMutation(s): 0 
Gene Names: kwaBECO55CA74_24530
UniProt
Find proteins for P0DW46 (Escherichia coli O55:H7 (strain RM12579 / EPEC))
Explore P0DW46 
Go to UniProtKB:  P0DW46
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DW46
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.324 (Depositor), 0.326 (DCC) 
  • R-Value Work:  0.276 (Depositor), 0.277 (DCC) 
  • R-Value Observed: 0.281 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.974α = 90
b = 163.974β = 90
c = 61.124γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
RAPDdata processing
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited StatesP30CA008748

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2026-05-20
    Changes: Database references