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- EMDB-49973: Cryo-EM structure of Local KwaA-KwaB complex -

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Basic information

Entry
Database: EMDB / ID: EMD-49973
TitleCryo-EM structure of Local KwaA-KwaB complex
Map dataCryo-EM density map for local KwaAB complex.
Sample
  • Complex: KwaA monomer bound to KwaB dimer
    • Protein or peptide: Kiwa protein KwaA
    • Protein or peptide: Kiwa protein KwaB
Keywordsantiphage / kiwa / ANTIVIRAL PROTEIN
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: 3.86 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: To Be Published
Title: Cryo-EM structure of Local KwaA-KwaB complex.
Authors: Zhang Z / Patel DJ
History
DepositionApr 2, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49973.png

Downloads & links

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Map

FileDownload / File: emd_49973.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map for local 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: 0.13
Minimum - Maximum-0.54302937 - 0.82039577
Average (Standard dev.)0.0015588532 (±0.012956154)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: Cryo-EM half B map for local KwaAB complex.

Fileemd_49973_half_map_1.map
AnnotationCryo-EM half B map for local KwaAB complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half A map for local KwaAB complex.

Fileemd_49973_half_map_2.map
AnnotationCryo-EM half A map for local KwaAB complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : KwaA monomer bound to KwaB dimer

EntireName: KwaA monomer bound to KwaB dimer
Components
  • Complex: KwaA monomer bound to KwaB dimer
    • Protein or peptide: Kiwa protein KwaA
    • Protein or peptide: Kiwa protein KwaB

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Supramolecule #1: KwaA monomer bound to KwaB dimer

SupramoleculeName: KwaA monomer bound to KwaB dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Kiwa protein KwaA

MacromoleculeName: Kiwa protein KwaA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.523566 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 FIARKKIDYK DDDDK

UniProtKB: Kiwa protein KwaA

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Macromolecule #2: Kiwa protein KwaB

MacromoleculeName: Kiwa protein KwaB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 36.976324 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 IAKDRLDEHH HHH H

UniProtKB: Kiwa protein KwaB

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Alphafold 3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 294296
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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