8ZSG | pdb_00008zsg

CryoEM Helical Structure of resting KomBC complex

• PDB DOI: https://doi.org/10.2210/pdb8ZSG/pdb
• EM Map EMD-60414: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-05 Released: 2025-12-10 
• Deposition Author(s): Feng, H., Shao, K., Tan, E.Y.J., Wu, B., Luo, M.
• Funding Organization(s): Ministry of Education (MoE, Singapore)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.66 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

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

• PubMed: 41638214 
• 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.
National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
School of Biological Sciences, Nanyang Technological University, Singapore 636921, Singapore.
Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
School of Biological Sciences, Nanyang Technological University, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore. Electronic address: [e-mail].
National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: [e-mail].
Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore; Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A12B12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 619.02 kDa 
• Atom Count: 43,668 
• Modeled Residue Count: 5,376 
• Deposited Residue Count: 5,376 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KomC, SIR2 domain protein, NADase	A [auth R], B [auth T], G [auth b], H [auth f], I [auth A], J [auth C], O [auth K], P [auth O], Q [auth B], R [auth D], W [auth L], X [auth P]	264	Escherichia coli	Mutation(s): 0  Gene Names: GRW56_02060, GRW57_01895

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
KomB, HAM-like protein, non-canonical purine NTP pyrophosphatase	C [auth V], D [auth X], E [auth Z], F [auth d], K [auth E], L [auth G], M [auth I], N [auth M], S [auth F], T [auth H], U [auth J], V [auth N]	184	Escherichia coli	Mutation(s): 0  Gene Names: GRW56_02065, GRW57_01900

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.66 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Feng, H., Shao, K., Tan, E.Y.J., Wu, B., Luo, M.

---

Funding Organization	Location	Grant Number
Ministry of Education (MoE, Singapore)	Singapore	--

Revision History  

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