[English] 日本語
Yorodumi
- EMDB-48564: Cryo-EM structure of KwaA-KwaB complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48564
TitleCryo-EM structure of KwaA-KwaB complex
Map dataCryo-EM density map of KwaAB complex
Sample
  • Complex: KwaA-KwaB COMPLEX
    • Protein or peptide: Kiwa protein KwaA
    • Protein or peptide: Kiwa protein KwaB
KeywordsKwaA-KwaB complex / anti-phage defense / IMMUNE SYSTEM
Function / homologyProtein of unknown function DUF4868 / : / Kiwa protein KwaB-like / : / defense response to virus / plasma membrane / Kiwa protein KwaA / Kiwa protein KwaB
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsZhang Z / Patel DJ
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48564.png

Downloads & links

-
Map

FileDownload / File: emd_48564.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map of KwaAB complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 396.48 Å		0.83 Å/pix.
x 480 pix.
= 396.48 Å		0.83 Å/pix.
x 480 pix.
= 396.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.111
Minimum - Maximum-0.5558859 - 0.92748916
Average (Standard dev.)0.0015362371 (±0.01526122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 396.47998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Cryo-EM half A map of KwaAB complex

Fileemd_48564_half_map_1.map
AnnotationCryo-EM half A map of KwaAB complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM half B map of KwaAB complex

Fileemd_48564_half_map_2.map
AnnotationCryo-EM half B map of KwaAB complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : KwaA-KwaB COMPLEX

EntireName: KwaA-KwaB COMPLEX
Components
  • Complex: KwaA-KwaB COMPLEX
    • Protein or peptide: Kiwa protein KwaA
    • Protein or peptide: Kiwa protein KwaB

-
Supramolecule #1: KwaA-KwaB COMPLEX

SupramoleculeName: KwaA-KwaB COMPLEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Kiwa protein KwaA

MacromoleculeName: Kiwa protein KwaA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 22.52659 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQRNTYNKVG LYILSLAMLF VFIIILTAKI PFCFTSDCSF IGLKKLVLTN IVPIVCFVFF LFSIYFYNRL KNITKYNGQD SVKITSCQS ESYESLTFLA TYIVPFMGFS FEDMQKNIAY LLLVVVIGII FIKTDKYYAN PTLALFGFKL YRVNILHPGS G ETKNLIAI ...String:
MQRNTYNKVG LYILSLAMLF VFIIILTAKI PFCFTSDCSF IGLKKLVLTN IVPIVCFVFF LFSIYFYNRL KNITKYNGQD SVKITSCQS ESYESLTFLA TYIVPFMGFS FEDMQKNIAY LLLVVVIGII FIKTDKYYAN PTLALFGFKL YRVNILHPGS G ETKNLIAI SNDVLKVDDN VYYSFFDEFV FIARKKI

UniProtKB: Kiwa protein KwaA

-
Macromolecule #2: Kiwa protein KwaB

MacromoleculeName: Kiwa protein KwaB / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 36.147453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTQQLKEKI SKIIDNFSGI RVVFTTTANE LKLSRIEGSA LNSIAEGFID KIKEDIINNE DLTSPLLSNF DDRKNALFKF DYEQYPEEF NKITQAIAIP PNSQDYYNPL NKFTDVKGII ILISGDNKCL ALYKNKTNLA VLRNSRKMFN LVPDPDGYLK Q LPNEILRL ...String:
MTTQQLKEKI SKIIDNFSGI RVVFTTTANE LKLSRIEGSA LNSIAEGFID KIKEDIINNE DLTSPLLSNF DDRKNALFKF DYEQYPEEF NKITQAIAIP PNSQDYYNPL NKFTDVKGII ILISGDNKCL ALYKNKTNLA VLRNSRKMFN LVPDPDGYLK Q LPNEILRL DFNYDLFSIG EDFYIKNHKT LETQMKFHQV IEAQAVIALN SLRDSLLIED ISGLEKSSRE ISFARKLAKI SK HSPVLGK IDTKTIIDYV SQHKYLSAIL QINEAGDKLL IKTKTSQKHF IKLMSDDYLQ SDLTKIIYMS IAKDRLDE

UniProtKB: Kiwa protein KwaB

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.73 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: AF3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73574
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more