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- EMDB-48562: Cryo-EM structure of KwaA with C4 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-48562
TitleCryo-EM structure of KwaA with C4 symmetry
Map dataCryo-EM half A map of KwaA with C4 symmetry
Sample
  • Complex: Cryo-EM structure of KwaA with C4 symmetry
    • Protein or peptide: Kiwa protein KwaA
KeywordsKwaA tetramer / C4 / anti-phage defense / IMMUNE SYSTEM
Function / homology: / defense response to virus / plasma membrane / Kiwa protein KwaA
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.28 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 KwaA with C4 symmetry
Authors: Zhang Z / Patel DJ
History
DepositionJan 8, 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_48562.png

Downloads & links

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Map

FileDownload / File: emd_48562.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM half A map of KwaA with C4 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 212.8 Å		1.06 Å/pix.
x 200 pix.
= 212.8 Å		1.06 Å/pix.
x 200 pix.
= 212.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.162
Minimum - Maximum-0.45162588 - 0.7574248
Average (Standard dev.)0.0018659085 (±0.024504142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 212.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM half A map of KwaA with C4 symmetry

Fileemd_48562_half_map_1.map
AnnotationCryo-EM half A map of KwaA with C4 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half A map of KwaA with C4 symmetry

Fileemd_48562_half_map_2.map
AnnotationCryo-EM half A map of KwaA with C4 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of KwaA with C4 symmetry

EntireName: Cryo-EM structure of KwaA with C4 symmetry
Components
  • Complex: Cryo-EM structure of KwaA with C4 symmetry
    • Protein or peptide: Kiwa protein KwaA

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Supramolecule #1: Cryo-EM structure of KwaA with C4 symmetry

SupramoleculeName: Cryo-EM structure of KwaA with C4 symmetry / 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: 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

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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: GATAN K3 (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / 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: AF3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 278569
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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