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- EMDB-67286: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with N... -

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Basic information

Entry
Database: EMDB / ID: EMD-67286
TitleCryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments
Map data
Sample
  • Complex: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments
    • Protein or peptide: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
    • Protein or peptide: KomC(H146N), a SIR2-domain NADase
  • Ligand: 2'-deoxyinosine 5'-triphosphate
  • Ligand: ADENOSINE MONOPHOSPHATE
KeywordsKomBC / NAD hydrolysis protein / IMMUNE SYSTEM
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXie W / Feng H / Luo M
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments
Authors: Xie W / Feng H / Luo M
History
DepositionNov 26, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67286.png

Downloads & links

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Map

FileDownload / File: emd_67286.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.234
Minimum - Maximum-0.56117296 - 1.2342453
Average (Standard dev.)0.00066803524 (±0.04159246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_67286_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_67286_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 : Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with N...

EntireName: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments
Components
  • Complex: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments
    • Protein or peptide: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
    • Protein or peptide: KomC(H146N), a SIR2-domain NADase
  • Ligand: 2'-deoxyinosine 5'-triphosphate
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with N...

SupramoleculeName: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase

MacromoleculeName: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.929131 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNIRFITRNR HKIKEINKIL SGTGVVVLAS EHSIDEIQTE NVHALIKDKL LKAFKLVGRP VFVEHTGLYI ESLNGFPGGL TQIFWDKLQ ADKFSQLLGT SENPRLVAKT IIGYCDSMKI YIFEGETQGT ISPVPKGPRD FQWDCIFIPD GESETFAEMG D RKNEISMR KKAFDKFKEY LLEGGK

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Macromolecule #2: KomC(H146N), a SIR2-domain NADase

MacromoleculeName: KomC(H146N), a SIR2-domain NADase / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 30.631842 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEQLLADYKK GNVILFVGAG VSMNLGLPSW SQLVDHIATE LGYDPDIYRT FGSALELAEY YKLKKGKIGP LRSWMDRMWH SSDIDINKS KVHEYIAKAN FPIIYTTNYD RWIETALSNY GKEYIKISSV SDIAKIDNNK TQIIKFNGDF DDDSSIVLDE T SYFQRLEF ...String:
MEQLLADYKK GNVILFVGAG VSMNLGLPSW SQLVDHIATE LGYDPDIYRT FGSALELAEY YKLKKGKIGP LRSWMDRMWH SSDIDINKS KVHEYIAKAN FPIIYTTNYD RWIETALSNY GKEYIKISSV SDIAKIDNNK TQIIKFNGDF DDDSSIVLDE T SYFQRLEF ETPLDIKFRS DVLGKSVLFI GYSLSDINIR LLFYKLSKLW KEQKLEEAQP KSYIFLPRPN PIQEEILEQW RI GMISSEN DNPGESLEEF LKNFVLV

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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: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 47.06 Å
Applied symmetry - Helical parameters - Δ&Phi: -79.93 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 208086
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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