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- PDB-9mrr: Cryo-EM structure of KwaA with C4 symmetry -

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Basic information

Entry
Database: PDB / ID: 9mrr
TitleCryo-EM structure of KwaA with C4 symmetry
ComponentsKiwa protein KwaA
KeywordsIMMUNE SYSTEM / KwaA tetramer / C4 / anti-phage defense
Function / homology: / defense response to virus / plasma membrane / Kiwa protein KwaA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.28 Å
AuthorsZhang, Z. / Patel, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA008748 United States
CitationJournal: Cell / Year: 2025
Title: Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites.
Authors: Zhiying Zhang / Thomas C Todeschini / Yi Wu / Roman Kogay / Ameena Naji / Joaquin Cardenas Rodriguez / Rupavidhya Mondi / Daniel Kaganovich / David W Taylor / Jack P K Bravo / Marianna ...Authors: Zhiying Zhang / Thomas C Todeschini / Yi Wu / Roman Kogay / Ameena Naji / Joaquin Cardenas Rodriguez / Rupavidhya Mondi / Daniel Kaganovich / David W Taylor / Jack P K Bravo / Marianna Teplova / Triana Amen / Eugene V Koonin / Dinshaw J Patel / Franklin L Nobrega /
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 ...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.
History
DepositionJan 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
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Revision 1.1May 20, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kiwa protein KwaA
B: Kiwa protein KwaA
C: Kiwa protein KwaA
D: Kiwa protein KwaA


Theoretical massNumber of molelcules
Total (without water)90,1064
Polymers90,1064
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Kiwa protein KwaA


Mass: 22526.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kwaA, ECO55CA74_24535 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW45
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of KwaA with C4 symmetry / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 278569 / Symmetry type: POINT

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