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- PDB-9v2m: Cryo-EM structure of KomBC Tetra-dimer -

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Basic information

Entry
Database: PDB / ID: 9v2m
TitleCryo-EM structure of KomBC Tetra-dimer
Components
  • NAD-dependent protein deacetylase
  • Xanthosine/inosine triphosphate pyrophosphatase
KeywordsCELL INVASION / KomB-KomC / dimer
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: 3.67 Å
AuthorsLi, Y. / Zheng, Q. / Li, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Cell / Year: 2026
Title: Filament-driven activation of the Kongming antiviral system by deoxyinosine triphosphate.
Authors: Xiangkai Zhen / Yu Li / Zihe Liu / Yang Huang / Xurong Wang / Shuying Xu / Yuchen Jiang / Fan Li / Jinfu Su / Qi Lai / Shaowei Li / Ningshao Xia / Qingbing Zheng / Songying Ouyang /
Abstract: Nucleotide-derived second messengers are frequently deployed by bacteria to activate effector proteins to mediate the immunity. The Kongming system uses deoxyinosine triphosphate (dITP) to trigger ...Nucleotide-derived second messengers are frequently deployed by bacteria to activate effector proteins to mediate the immunity. The Kongming system uses deoxyinosine triphosphate (dITP) to trigger nicotinamide adenine dinucleotide (NAD) depletion via the Sir2-domain protein KomC. We reveal that dITP binding to the KomB-KomC (KomBC) complex stabilizes KomB dimerization, initiating hierarchical allosteric changes. This drives KomBC filament assembly, which is essential for activating the NADase activity of KomC. Cryo-EM structures of apo-, dITP-bound, NAD-bound and postcatalytic KomBC filaments show the structural landscape of how dITP-induced remodeling reshapes the catalytic pocket of KomC, enabling NAD hydrolysis. Mutagenesis confirms that filament assembly and allostery are critical for catalysis. These findings elucidate the structural basis for the recognition of the nucleotide derivative signaling molecule, the assembly and the filament-mediated allosteric activation mechanism in prokaryotic immunity and a distinct variation of Sir2 NADase activation.
History
DepositionMay 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
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Revision 1.1Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Q: Xanthosine/inosine triphosphate pyrophosphatase
R: Xanthosine/inosine triphosphate pyrophosphatase
S: Xanthosine/inosine triphosphate pyrophosphatase
T: Xanthosine/inosine triphosphate pyrophosphatase
U: NAD-dependent protein deacetylase
V: NAD-dependent protein deacetylase
W: NAD-dependent protein deacetylase
X: NAD-dependent protein deacetylase


Theoretical massNumber of molelcules
Total (without water)411,06216
Polymers411,06216
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.: 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


Mass: 31370.715 Da / Num. of mol.: 8
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 dimer / 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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
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: 60 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: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119591 / Symmetry type: POINT

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