8ZSH | pdb_00008zsh

Cryo-EM Helical Structure of dITP-activated KomBC complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZSH

This is version 1.1 of the entry. See complete history

Literature

Filament-mediated repurposing of toxic dITP for immunity in the Kongming system.

Feng, H.Shao, K.Zeng, Z.Tan, E.Y.J.Hu, Z.Zhao, R.Rao, J.Shi, J.Chen, Z.Redondo, R.P.Wu, B.Han, W.Luo, M.

(2026) Mol Cell 86: 1148-1163.e5

  • DOI: https://doi.org/10.1016/j.molcel.2026.01.027
  • Primary Citation Related Structures: 
    8ZSF, 8ZSG, 8ZSH, 9XVC

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore.

Macromolecule Content 

  • Total Structure Weight: 833.62 kDa 
  • Atom Count: 58,704 
  • Modeled Residue Count: 7,168 
  • Deposited Residue Count: 7,168 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase184Escherichia coliMutation(s): 0 
Gene Names: GRW56_02065GRW57_01900
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
KomC, SIR2 domain protein, NADase264Escherichia coliMutation(s): 0 
Gene Names: GRW56_02060GRW57_01895

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y43
(Subject of Investigation/LOI)

Query on Y43



Download:Ideal Coordinates CCD File
AB [auth W]
CB [auth U]
EB [auth f]
GA [auth A]
GB [auth Z]
AB [auth W],
CB [auth U],
EB [auth f],
GA [auth A],
GB [auth Z],
IA [auth B],
IB [auth V],
KA [auth C],
KB [auth X],
MA [auth D],
OA [auth J],
QA [auth I],
SA [auth K],
UA [auth L],
WA [auth Y],
YA [auth e]
2'-deoxyinosine 5'-triphosphate
C10 H15 N4 O13 P3
UFJPAQSLHAGEBL-RRKCRQDMSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
BB [auth W]
DB [auth U]
FB [auth f]
HA [auth A]
HB [auth Z]
BB [auth W],
DB [auth U],
FB [auth f],
HA [auth A],
HB [auth Z],
JA [auth B],
JB [auth V],
LA [auth C],
LB [auth X],
NA [auth D],
PA [auth J],
RA [auth I],
TA [auth K],
VA [auth L],
XA [auth Y],
ZA [auth e]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2026-06-24
    Changes: Data collection, Database references, Structure summary