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- PDB-9v0z: Cryo-EM structure of KomBC Tetramer -

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Basic information

Entry
Database: PDB / ID: 9v0z
TitleCryo-EM structure of KomBC Tetramer
Components
  • NAD-dependent protein deacetylase
  • Xanthosine/inosine triphosphate pyrophosphatase
KeywordsCELL INVASION / Cryo-EM structure of KomB-KomC Oligomer
Function / homology
Function and homology information


nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / cytoplasm
Similarity search - Function
Ham1-like protein / Ham1 family / Inosine triphosphate pyrophosphatase-like / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
XTP/dITP diphosphohydrolase / NAD-dependent protein deacetylase
Similarity search - Component
Biological speciesArchangium gephyra (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsLi, Y. / Zheng, Q. / Li, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of KomB-KomC Oligomer
Authors: Li, Y. / Zheng, Q. / Li, S.
History
DepositionMay 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 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

Downloads & links

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Assembly

Deposited unit
A: Xanthosine/inosine triphosphate pyrophosphatase
B: Xanthosine/inosine triphosphate pyrophosphatase
C: Xanthosine/inosine triphosphate pyrophosphatase
D: Xanthosine/inosine triphosphate pyrophosphatase
E: NAD-dependent protein deacetylase
F: NAD-dependent protein deacetylase
G: NAD-dependent protein deacetylase
H: NAD-dependent protein deacetylase


Theoretical massNumber of molelcules
Total (without water)205,5318
Polymers205,5318
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
Xanthosine/inosine triphosphate pyrophosphatase


Mass: 20012.025 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archangium gephyra (bacteria) / Gene: AA314_06977 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAC8QDB0
#2: Protein
NAD-dependent protein deacetylase


Mass: 31370.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archangium gephyra (bacteria) / Gene: AA314_06978 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAC8TGL7
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: KomB-KomC Oligomer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Archangium gephyra (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213475 / Symmetry type: POINT

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