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- PDB-9v12: Helical structure of KomBCMUT in complex with dITP and NAD -

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Basic information

Entry
Database: PDB / ID: 9v12
TitleHelical structure of KomBCMUT in complex with dITP and NAD
Components
  • NAD-dependent protein deacetylase
  • Xanthosine/inosine triphosphate pyrophosphatase
KeywordsCELL INVASION / Cryo-EM / Sir2
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2'-deoxyinosine 5'-triphosphate / XTP/dITP diphosphohydrolase / NAD-dependent protein deacetylase
Similarity search - Component
Biological speciesArchangium gephyra (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsLi, Y. / Zheng, Q. / Li, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Helical structure of KomBCMUT in complex with dITP and NAD
Authors: Li, Y. / Zheng, Q. / Li, S.
History
DepositionMay 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 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
I: Xanthosine/inosine triphosphate pyrophosphatase
K: Xanthosine/inosine triphosphate pyrophosphatase
M: Xanthosine/inosine triphosphate pyrophosphatase
O: Xanthosine/inosine triphosphate pyrophosphatase
R: Xanthosine/inosine triphosphate pyrophosphatase
T: Xanthosine/inosine triphosphate pyrophosphatase
V: Xanthosine/inosine triphosphate pyrophosphatase
X: Xanthosine/inosine triphosphate pyrophosphatase
i: NAD-dependent protein deacetylase
j: NAD-dependent protein deacetylase
k: NAD-dependent protein deacetylase
l: NAD-dependent protein deacetylase
m: NAD-dependent protein deacetylase
n: NAD-dependent protein deacetylase
o: NAD-dependent protein deacetylase
p: NAD-dependent protein deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)419,94940
Polymers410,18116
Non-polymers9,76824
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.: 8
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 / SIR2-like protein


Mass: 31260.621 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archangium gephyra (bacteria) / Gene: AA314_06978, ATI61_102412 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAC8TGL7
#3: Chemical
ChemComp-Y43 / 2'-deoxyinosine 5'-triphosphate


Mass: 492.166 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N4O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: KomB-KomCmut in complex with dITP and NAD / Type: COMPLEX / Entity ID: #2, #1 / 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

EM software
IDNameCategory
1RELIONparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 84.33 ° / Axial rise/subunit: 49.31 Å / Axial symmetry: C2
3D reconstructionResolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 597778 / Symmetry type: HELICAL

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