9WHU | pdb_00009whu

Structure of Klebsiella pneumoniae trypsin-HamAB bound with DNA, trimer

• PDB DOI: https://doi.org/10.2210/pdb9WHU/pdb
• NAKB: 9WHU
• EM Map EMD-65977: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-08-27 Released: 2026-06-03 
• Deposition Author(s): Huang, P.P., Liu, J.X., Shen, L.B., Chen, M.R., Xiao, Y.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The antiphage mechanism of a widespread trypsin-MBL defense module.

Huang, P., Liu, J., Guo, L., Xu, D., Shen, L., Yan, P., Tong, C., Fei, W., Cheng, M., Li, Z., Lu, M., Zhang, L., Wu, N., Qi, L.W., Xiao, Y., Chen, M.

(2026) Nat Chem Biol 

• PubMed: 42243536 
• DOI: https://doi.org/10.1038/s41589-026-02252-8
• Primary Citation Related Structures: 
  9WH1, 9WHK, 9WHU


• PubMed Abstract: 
  

  Protease-mediated activation of immune effectors is an evolutionarily conserved mechanism. This study identifies a widespread trypsin-MBL (metallo-β-lactamase) module as a core effector in diverse antiviral bacterial immune systems, such as Hachiman, AVAST and Argonaute. Focusing on the Hachiman-associated trypsin-MBL system, we show that trypsin•HamAB protease activity is inhibited by ATP, while MBL is an autoinhibited DNase with two insertion loops obstructing its catalytic site. Upon infection, trypsin•HamAB senses foreign DNA and hydrolyzes ATP, activating trypsin-like activity, which specifically cleaves MBL at the insertion loops to release repression. The activated MBL depletes DNA and arrests host cell growth. Cryo-electron microscopy structures of trypsin•HamAB-DNA reveal that DNA binding and ATP hydrolysis trigger HamAB oligomerization and trypsin-like domain release, enabling its activation. Our work elucidates a conserved immune mechanism wherein proteolytic activation of a nuclease enables robust immunity against phage while multilayered controls prevent self-toxicity, expanding the repertoire of immune processes governed by regulatory proteolysis.

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Organizational Affiliation: 
• State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China.
Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China.
Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, China.
Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China.
Fudan University Phage Institute, Zhongshan Hospital Fudan University, Shanghai, China. [e-mail].
CreatiPhage Biotechnology, Ltd., Co., Shanghai, China. [e-mail].
State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China. [e-mail].
School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China. [e-mail].
Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, China. [e-mail].
School of Traditional Chinese Medicine, Shenyang Pharmaceutical University, Shenyang, China. [e-mail].
State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China. [e-mail].
Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China. [e-mail].
Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, China. [e-mail].
State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China. [e-mail].
Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China. [e-mail].
Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 483.02 kDa 
• Atom Count: 28,311 
• Modeled Residue Count: 3,428 
• Deposited Residue Count: 4,166 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-bacteriophage protein A/HamA C-terminal domain-containing protein	A, C [auth D], F [auth G]	528	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: SAMEA4873653_00088
UniProt
Find proteins for A0A486PDC8 (Klebsiella pneumoniae) Explore A0A486PDC8  Go to UniProtKB:  A0A486PDC8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase theta (Helicase domain only)	B, D [auth E], G [auth H]	853	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: B6I68_29715, SAMEA4873653_00087
UniProt
Find proteins for A0A486PCQ5 (Klebsiella pneumoniae) Explore A0A486PCQ5  Go to UniProtKB:  A0A486PCQ5

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')	E [auth F]	7	Klebsiella pneumoniae

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')	H [auth I], I [auth C]	8	Klebsiella pneumoniae

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Huang, P.P., Liu, J.X., Shen, L.B., Chen, M.R., Xiao, Y.B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release
  
• Version 1.1: 2026-07-29
  Changes: Data collection, Database references