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- EMDB-64788: Helical structure of KomBC in complex with dITP -

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Basic information

Entry
Database: EMDB / ID: EMD-64788
TitleHelical structure of KomBC in complex with dITP
Map data
Sample
  • Complex: KomBC filament with dITP
    • Protein or peptide: Xanthosine/inosine triphosphate pyrophosphatase
    • Protein or peptide: NAD-dependent protein deacetylase
  • Ligand: 2'-deoxyinosine 5'-triphosphate
  • Ligand: ZINC ION
KeywordsKomBc / dITP / Sir2 / 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: 3.04 Å
AuthorsLi Y / Zheng Q / Li S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Helical structure of KomBC in complex with dITP
Authors: Li Y / Zheng Q / Li S
History
DepositionMay 25, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64788.png

Downloads & links

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Map

FileDownload / File: emd_64788.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 448 pix.
= 348.544 Å		0.78 Å/pix.
x 448 pix.
= 348.544 Å		0.78 Å/pix.
x 448 pix.
= 348.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.08059178 - 0.264816
Average (Standard dev.)0.0002794344 (±0.0136405295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 348.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_64788_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #2

Fileemd_64788_additional_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64788_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64788_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : KomBC filament with dITP

EntireName: KomBC filament with dITP
Components
  • Complex: KomBC filament with dITP
    • Protein or peptide: Xanthosine/inosine triphosphate pyrophosphatase
    • Protein or peptide: NAD-dependent protein deacetylase
  • Ligand: 2'-deoxyinosine 5'-triphosphate
  • Ligand: ZINC ION

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Supramolecule #1: KomBC filament with dITP

SupramoleculeName: KomBC filament with dITP / 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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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 49.25 Å
Applied symmetry - Helical parameters - Δ&Phi: 83.37 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1574792
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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