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- PDB-8zsf: CryoEM Helical Structure of KomC -

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Basic information

Entry
Database: PDB / ID: 8zsf
TitleCryoEM Helical Structure of KomC
ComponentsSir2 family NAD-dependent protein deacetylase
KeywordsIMMUNE SYSTEM / NADase / Filament / CryoEM
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsFeng, H. / Shao, K. / Luo, M.
Funding support Singapore, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
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Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Jun 24, 2026Group: Data collection / Database references / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Sir2 family NAD-dependent protein deacetylase
A: Sir2 family NAD-dependent protein deacetylase
C: Sir2 family NAD-dependent protein deacetylase
B: Sir2 family NAD-dependent protein deacetylase
K: Sir2 family NAD-dependent protein deacetylase
E: Sir2 family NAD-dependent protein deacetylase
I: Sir2 family NAD-dependent protein deacetylase
G: Sir2 family NAD-dependent protein deacetylase
L: Sir2 family NAD-dependent protein deacetylase
F: Sir2 family NAD-dependent protein deacetylase
J: Sir2 family NAD-dependent protein deacetylase
H: Sir2 family NAD-dependent protein deacetylase


Theoretical massNumber of molelcules
Total (without water)367,87112
Polymers367,87112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Sir2 family NAD-dependent protein deacetylase / KomC / SIR2-like domain proteins


Mass: 30655.889 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GRW56_02060, GRW57_01895 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A2Y0UIK6
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Filament of tetrameric KomC / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 367.2 kDa/nm / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 92 ° / Axial rise/subunit: 45.2 Å / Axial symmetry: C1
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 487493 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00526616
ELECTRON MICROSCOPYf_angle_d0.92635988
ELECTRON MICROSCOPYf_dihedral_angle_d6.2973444
ELECTRON MICROSCOPYf_chiral_restr0.0583876
ELECTRON MICROSCOPYf_plane_restr0.0084560

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