23SF | pdb_000023sf

Cryo-EM structure of icosahedrally averaged bacteriophage RAN69 capsid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 23SF

This is version 1.1 of the entry. See complete history

Literature

Near-complete cryo-EM structure of the Klebsiella pneumoniae podophage RAN69 reveals tail fiber-spike interface and a divergent pre-ejectosome.

Ruan, Z.Hu, H.Wang, A.Shao, Q.Li, X.Xie, L.Sun, Z.Yu, J.Fang, Q.

(2026) Structure 

  • DOI: https://doi.org/10.1016/j.str.2026.05.010
  • Primary Citation Related Structures: 
    23SF, 23SG, 23SH

  • PubMed Abstract: 

    Carbapenem-resistant Klebsiella pneumoniae is a critical-priority pathogen, underscoring the need for alternatives to antibiotics. Bacteriophages are promising agents, yet high-resolution structures of K. pneumoniae phages are scarce. Here, we report near-complete cryo-electron microscopic reconstructions of the K. pneumoniae podophage RAN69 at 3.0-3.4 Å resolution, enabling atomic models for 12 structural components. Complete in situ structures of the long tail fiber (gp9 trimer) and distal tail spike (gp1 trimer) are resolved, revealing a previously unknown binding interface in which the gp1 N-terminal arm wedges between spike-binding domains of gp9. The pre-ejectosome forms a conserved double-layered assembly (gp10 tetramer over gp11 octamer), tethered to the portal by an octameric gp12 that inserts long helices into the portal barrel, with gp20 reinforcing gp11 interfaces. Divergent folds in gp10 and a lysozyme-like gp11 peripheral domain suggest adaptation to host envelopes. These structures advance our understanding of podophage assembly.


  • Organizational Affiliation
    • School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China.

Macromolecule Content 

  • Total Structure Weight: 308.35 kDa 
  • Atom Count: 21,507 
  • Modeled Residue Count: 2,782 
  • Deposited Residue Count: 2,801 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
decoration protein gp6A,
B [auth C]
124Klebsiella phage RAN69Mutation(s): 0 
UniProt
Find proteins for A0AAE9HEE2 (Klebsiella phage FK1979)
Explore A0AAE9HEE2 
Go to UniProtKB:  A0AAE9HEE2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAE9HEE2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
major capsid protein gp17339Klebsiella phage RAN69Mutation(s): 0 
UniProt
Find proteins for A0AAE9KT08 (Klebsiella phage FK1979)
Explore A0AAE9KT08 
Go to UniProtKB:  A0AAE9KT08
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAE9KT08
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
decoration protein gp5I [auth G],
K [auth J],
L
60Klebsiella phage RAN69Mutation(s): 0 
UniProt
Find proteins for A0AAE9HDJ1 (Klebsiella phage FK1979)
Explore A0AAE9HDJ1 
Go to UniProtKB:  A0AAE9HDJ1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAE9HDJ1
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaJCYJ20250604174416022
Other governmentChinaA2402025
National Natural Science Foundation of China (NSFC)China32371285

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-27
    Type: Initial release
  • Version 1.1: 2026-07-01
    Changes: Data collection, Database references