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- EMDB-64676: Helical structure of KomBC in complex with dITP and NAM -

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Basic information

Entry
Database: EMDB / ID: EMD-64676
TitleHelical structure of KomBC in complex with dITP and NAM
Map data
Sample
  • Complex: KomB-KomC in complex with dITP and NAM
    • Protein or peptide: Xanthosine/inosine triphosphate pyrophosphatase
    • Protein or peptide: NAD-dependent protein deacetylase
  • Ligand: 2'-deoxyinosine 5'-triphosphate
  • Ligand: ZINC ION
  • Ligand: NICOTINAMIDE
Keywordsfilament / KomBC in complex with dITP and NAM / CELL INVASION
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)
Methodhelical reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsLi Y / Zheng Q / Li S / Wu Y
Funding support1 items
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 19, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64676.png

Downloads & links

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Map

FileDownload / File: emd_64676.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 448 pix.
= 291.2 Å		0.65 Å/pix.
x 448 pix.
= 291.2 Å		0.65 Å/pix.
x 448 pix.
= 291.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.18199944 - 0.3763215
Average (Standard dev.)0.0008843329 (±0.017022641)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 291.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_64676_additional_1.map
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Additional map: #2

Fileemd_64676_additional_2.map
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Half map: #2

Fileemd_64676_half_map_1.map
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Half map: #1

Fileemd_64676_half_map_2.map
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Sample components

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Entire : KomB-KomC in complex with dITP and NAM

EntireName: KomB-KomC in complex with dITP and NAM
Components
  • Complex: KomB-KomC in complex with dITP and NAM
    • Protein or peptide: Xanthosine/inosine triphosphate pyrophosphatase
    • Protein or peptide: NAD-dependent protein deacetylase
  • Ligand: 2'-deoxyinosine 5'-triphosphate
  • Ligand: ZINC ION
  • Ligand: NICOTINAMIDE

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Supramolecule #1: KomB-KomC in complex with dITP and NAM

SupramoleculeName: KomB-KomC in complex with dITP and NAM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Archangium gephyra (bacteria)

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Macromolecule #1: Xanthosine/inosine triphosphate pyrophosphatase

MacromoleculeName: Xanthosine/inosine triphosphate pyrophosphatase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Archangium gephyra (bacteria)
Molecular weightTheoretical: 20.012025 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAPTWFYNTT NSEKLRELQH VLGGSAKLGY LTAKVTEILD VDLETVIRAK AIAAYRAVRV PVIVEHGALC IDALNGLPGA LVKPFWESL DTRLCEVIPA GQRTARARGA LCYCDGRERH VLIEETEGEI APSARGTGGF HWDPIFIPKG QTRTFAEMSL D EKLSFSPL GRLHTRLRTE LGL

UniProtKB: XTP/dITP diphosphohydrolase

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Macromolecule #2: NAD-dependent protein deacetylase

MacromoleculeName: NAD-dependent protein deacetylase / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Archangium gephyra (bacteria)
Molecular weightTheoretical: 31.370715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTLTLSEAA PLLKKEFREG RLIPFLGAGF SKPLKLPDGS QLIASLAKTL GFEPELFDMH GRFEQLAEFF AISAPNRLQR LVYEMSLSF DSAEAEALRE KSPMHRALAA LDWRTIYTTN YDKHVEGALR DAGKQAAVLA SFADFQGPRA RDVCEVIKFH G TLDQPDTI ...String:
MTTLTLSEAA PLLKKEFREG RLIPFLGAGF SKPLKLPDGS QLIASLAKTL GFEPELFDMH GRFEQLAEFF AISAPNRLQR LVYEMSLSF DSAEAEALRE KSPMHRALAA LDWRTIYTTN YDKHVEGALR DAGKQAAVLA SFADFQGPRA RDVCEVIKFH G TLDQPDTI VLTESSYFQR MALDAPPDQR LRADLLANSF LFIGYSFSDT NIRYIWYRMN QLREQSQLGV KHSQARRCFF AT HGAGLVQ PDILQQWNID VIQLDPTDKS ASVARLLESI A

UniProtKB: NAD-dependent protein deacetylase

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Macromolecule #3: 2'-deoxyinosine 5'-triphosphate

MacromoleculeName: 2'-deoxyinosine 5'-triphosphate / type: ligand / ID: 3 / Number of copies: 8 / Formula: Y43
Molecular weightTheoretical: 492.166 Da
Chemical component information

ChemComp-Y43:
2'-deoxyinosine 5'-triphosphate

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: NICOTINAMIDE

MacromoleculeName: NICOTINAMIDE / type: ligand / ID: 5 / Number of copies: 8 / Formula: NCA
Molecular weightTheoretical: 122.125 Da
Chemical component information

ChemComp-NCA:
NICOTINAMIDE / medication*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 49.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 83.73 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1526618
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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