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- PDB-9o0i: Cryo-EM structure of Local KwaA-KwaB complex -

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Basic information

Entry
Database: PDB / ID: 9o0i
TitleCryo-EM structure of Local KwaA-KwaB complex
Components
  • Kiwa protein KwaA
  • Kiwa protein KwaB
KeywordsANTIVIRAL PROTEIN / antiphage / kiwa
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.86 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: To Be Published
Title: Cryo-EM structure of Local KwaA-KwaB complex.
Authors: Zhang, Z. / Patel, D.J.
History
DepositionApr 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Kiwa protein KwaA
H: Kiwa protein KwaB
J: Kiwa protein KwaB


Theoretical massNumber of molelcules
Total (without water)97,4763
Polymers97,4763
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: 23523.566 Da / Num. of mol.: 1
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
#2: Protein Kiwa protein KwaB


Mass: 36976.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kwaB, ECO55CA74_24530 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW46
Has protein modificationY

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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: KwaA monomer bound to KwaB dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
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: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 58.73 e/Å2 / Film or detector model: FEI FALCON IV (4k 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: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 294296 / Symmetry type: POINT
RefinementHighest resolution: 3.86 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046796
ELECTRON MICROSCOPYf_angle_d0.9629164
ELECTRON MICROSCOPYf_dihedral_angle_d5.396883
ELECTRON MICROSCOPYf_chiral_restr0.0551061
ELECTRON MICROSCOPYf_plane_restr0.0061151

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