9K4B | pdb_00009k4b

Cryo-EM structure of depolymerase S2-4 from Klebsiella phage K64-1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Characterization of the phage Phi K64 depolymerase S2-4 and its therapeutic effect against K1 serotype Klebsiella pneumoniae.

Zhao, R.Du, T.Ji, Y.Ren, Z.Jiang, S.Ru, H.Gu, J.

(2026) Microbiol Res 307: 128475-128475

  • DOI: https://doi.org/10.1016/j.micres.2026.128475
  • Primary Citation of Related Structures:  
    9K4A, 9K4B

  • PubMed Abstract: 

    The infection rate and drug resistance of Klebsiella pneumoniae containing capsular polysaccharides (CPSs) have been increasing annually, resulting in severe human and animal infections. Depolymerases derived from bacteriophages can degrade CPSs and thus hold potential for treating bacterial infections. However, little is known about the mechanism by which K. pneumoniae phage depolymerases hydrolyze CPSs. In this study, the S2-4 encoded by the phage ΦK64 was identified as a potent depolymerase against K1 serotype Klebsiella CPSs. Cryo-electron microscopy structural analysis revealed that S2-4 forms a homotrimer with a spindle-like structure comprising a particle-binding domain, a core receptor-binding domain, an insertion domain, and a C-terminal domain. The results of structural assays suggest that S2-4 possesses multiple catalytic centers, which may contribute to its potent depolymerase activity. S2-4 inhibited K. pneumoniae biofilm formation, disrupted preformed biofilms, and enhanced macrophage adhesion and phagocytosis in depolymerase-treated bacteria. In a murine model, a single dose of 5 µg of S2-4 provided full protection against bacterial infection, underscoring the potent depolymerase activity of S2-4. These results indicate that S2-4 is a potent depolymerase against K1 serotype Klebsiella CPSs and has the potential to be a promising candidate for the clinical control of K. pneumoniae infections.


  • Organizational Affiliation
    • State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory of Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, PR China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Depolymerase, capsule K1-specific
A, B, C
922Klebsiella phage K64-1Mutation(s): 0 
Gene Names: S2-4
UniProt
Find proteins for A0A0A8J8T2 (Klebsiella phage K64-1)
Explore A0A0A8J8T2 
Go to UniProtKB:  A0A0A8J8T2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A8J8T2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32072824
National Natural Science Foundation of China (NSFC)China32222083

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-25
    Type: Initial release