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- EMDB-60415: Cryo-EM Helical Structure of dITP-activated KomBC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60415
TitleCryo-EM Helical Structure of dITP-activated KomBC complex
Map data
Sample
  • Complex: Filament of octomeric HAM-SIR2 with dITP
    • Protein or peptide: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
    • Protein or peptide: KomC, SIR2 domain protein, NADase
  • Ligand: 2'-deoxyinosine 5'-triphosphate
  • Ligand: MAGNESIUM ION
KeywordsBacterial immunity / NADase / Filament / CryoEM. / IMMUNE SYSTEM
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHao F / Eddie T / Kai S / Bin W / Min L
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Cryo-EM Helical Structure of dITP-activated KomBC complex
Authors: Hao F / Eddie T / Bin W / Min L
History
DepositionJun 5, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60415.png

Downloads & links

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Map

FileDownload / File: emd_60415.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 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: 0.012
Minimum - Maximum-0.043359596 - 0.07020652
Average (Standard dev.)0.00039605342 (±0.0034043582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60415_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_60415_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 : Filament of octomeric HAM-SIR2 with dITP

EntireName: Filament of octomeric HAM-SIR2 with dITP
Components
  • Complex: Filament of octomeric HAM-SIR2 with dITP
    • Protein or peptide: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
    • Protein or peptide: KomC, SIR2 domain protein, NADase
  • Ligand: 2'-deoxyinosine 5'-triphosphate
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Filament of octomeric HAM-SIR2 with dITP

SupramoleculeName: Filament of octomeric HAM-SIR2 with dITP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 824 kDa/nm

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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: 16 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.929131 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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, SIR2 domain protein, NADase

MacromoleculeName: KomC, SIR2 domain protein, NADase / type: protein_or_peptide / ID: 2 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 30.655889 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEQLLADYKK GNVILFVGAG VSMNLGLPSW SQLVDHIATE LGYDPDIYRT FGSALELAEY YKLKKGKIGP LRSWMDRMWH SSDIDINKS KVHEYIAKAN FPIIYTTNYD RWIETALSNY GKEYIKISSV SDIAKIDNNK TQIIKFHGDF DDDSSIVLDE T SYFQRLEF ...String:
MEQLLADYKK GNVILFVGAG VSMNLGLPSW SQLVDHIATE LGYDPDIYRT FGSALELAEY YKLKKGKIGP LRSWMDRMWH SSDIDINKS KVHEYIAKAN FPIIYTTNYD RWIETALSNY GKEYIKISSV SDIAKIDNNK TQIIKFHGDF 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: 16 / Formula: Y43
Molecular weightTheoretical: 492.166 Da
Chemical component information

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

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 16 / Formula: MG
Molecular weightTheoretical: 24.305 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: 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: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: 47.48 Å
Applied symmetry - Helical parameters - Δ&Phi: 78.41 °
Applied symmetry - Helical parameters - Axial symmetry: D2 (2x2 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 335058
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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