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- EMDB-60414: CryoEM Helical Structure of resting KomBC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60414
TitleCryoEM Helical Structure of resting KomBC complex
Map data
Sample
  • Complex: Filament of octomeric HAM-SIR2
    • Protein or peptide: KomC, SIR2 domain protein, NADase
    • Protein or peptide: KomB, HAM-like protein, non-canonical purine NTP pyrophosphatase
KeywordsBacterial immunity / NADase / Filament / CryoEM / IMMUNE SYSTEM
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsFeng H / Shao K / Tan EYJ / Wu B / Luo M
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Mol Cell / Year: 2026
Title: Filament-mediated repurposing of toxic dITP for immunity in the Kongming system.
Authors: Hao Feng / Kai Shao / Zhifeng Zeng / Eddie Yong Jun Tan / Zeyu Hu / Ruiliang Zhao / Jikai Rao / Jian Shi / Zhuojian Chen / Rafael Pinilla Redondo / Bin Wu / Wenyuan Han / Min Luo /
Abstract: Abortive infection systems protect bacteria by triggering self-destruction in response to phage attack. Most known systems rely on stable cyclic nucleotides that accumulate to stoichiometric levels ...Abortive infection systems protect bacteria by triggering self-destruction in response to phage attack. Most known systems rely on stable cyclic nucleotides that accumulate to stoichiometric levels to activate effectors; the Kongming (Kom) system employs the toxic metabolite deoxyinosine triphosphate (dITP) as its signaling molecule. Here, we show that the Escherichia coli KomB-KomC (KomBC) complex forms a preassembled filament that remains inactive until dITP binding induces cooperative allosteric activation. KomB, a homolog of the nucleotide-hydrolyzing enzyme HAM1, has lost catalytic activity but evolved a high-affinity, hydrolysis-resistant binding pocket for dITP. Interestingly, substoichiometric dITP binding is sufficient to activate adjacent KomC NADase domains, which propagate activation cooperatively along the filament. This filament-based architecture enables ultrasensitive, long-range allosteric signaling in response to a low-abundance and short-lived metabolite. Our findings reveal an ultrasensitive immune strategy that transforms a toxic byproduct into a robust antiviral trigger, expanding the known repertoire of bacterial defense strategies.
History
DepositionJun 5, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60414.png

Downloads & links

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Map

FileDownload / File: emd_60414.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: 0.2
Minimum - Maximum-0.33320382 - 0.8207888
Average (Standard dev.)0.0014881075 (±0.03451758)
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: #2

Fileemd_60414_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_60414_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 : Filament of octomeric HAM-SIR2

EntireName: Filament of octomeric HAM-SIR2
Components
  • Complex: Filament of octomeric HAM-SIR2
    • Protein or peptide: KomC, SIR2 domain protein, NADase
    • Protein or peptide: KomB, HAM-like protein, non-canonical purine NTP pyrophosphatase

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Supramolecule #1: Filament of octomeric HAM-SIR2

SupramoleculeName: Filament of octomeric HAM-SIR2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 618 kDa/nm

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Macromolecule #1: KomC, SIR2 domain protein, NADase

MacromoleculeName: KomC, SIR2 domain protein, NADase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / 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 #2: KomB, HAM-like protein, non-canonical purine NTP pyrophosphatase

MacromoleculeName: KomB, HAM-like protein, non-canonical purine NTP pyrophosphatase
type: protein_or_peptide / ID: 2 / Number of copies: 12 / 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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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: 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: 47.11 Å
Applied symmetry - Helical parameters - Δ&Phi: 68.32 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3
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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