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- EMDB-64731: Cryo-EM structure of KomBC Tetra-tetramer -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64731
TitleCryo-EM structure of KomBC Tetra-tetramer
Map data
Sample
  • Complex: KomB-KomC Tetramer
    • Protein or peptide: Xanthosine/inosine triphosphate pyrophosphatase
    • Protein or peptide: NAD-dependent protein deacetylase
KeywordsCryo-EM / KomB-KomC / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLi Y / Zheng Q / Li S / Wu Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of KomB-KomC Tetramer
Authors: Li Y / Zheng Q / Li S
History
DepositionMay 20, 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_64731.png

Downloads & links

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Map

FileDownload / File: emd_64731.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 298.752 Å		0.78 Å/pix.
x 384 pix.
= 298.752 Å		0.78 Å/pix.
x 384 pix.
= 298.752 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: 0.1
Minimum - Maximum-0.0023724227 - 2.178251
Average (Standard dev.)0.004211961 (±0.044345837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 298.752 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64731_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64731_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : KomB-KomC Tetramer

EntireName: KomB-KomC Tetramer
Components
  • Complex: KomB-KomC Tetramer
    • Protein or peptide: Xanthosine/inosine triphosphate pyrophosphatase
    • Protein or peptide: NAD-dependent protein deacetylase

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Supramolecule #1: KomB-KomC Tetramer

SupramoleculeName: KomB-KomC Tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 16 / 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: 16 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 328747
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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