23SG | pdb_000023sg

The composite Cryo-EM structure of bacteriophage RAN69 pre-ejectosome-portal complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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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: 562.96 kDa 
  • Atom Count: 35,335 
  • Modeled Residue Count: 4,591 
  • Deposited Residue Count: 5,182 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
gp11A [auth N],
E [auth G]
893Klebsiella phage RAN69Mutation(s): 0 
UniProt
Find proteins for A0AAE9HH46 (Klebsiella phage FK1979)
Explore A0AAE9HH46 
Go to UniProtKB:  A0AAE9HH46
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UniProt GroupA0AAE9HH46
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
gp12B [auth X],
C [auth a]
195Klebsiella phage RAN69Mutation(s): 0 
UniProt
Find proteins for A0ABZ0ZXM7 (Klebsiella phage KA)
Explore A0ABZ0ZXM7 
Go to UniProtKB:  A0ABZ0ZXM7
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UniProt GroupA0ABZ0ZXM7
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
gp10D [auth S]1,239Klebsiella phage RAN69Mutation(s): 0 
UniProt
Find proteins for V9QJ34 (Klebsiella phage F19)
Explore V9QJ34 
Go to UniProtKB:  V9QJ34
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UniProt GroupV9QJ34
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
portal gp19F [auth d],
G [auth A],
H [auth D]
531Klebsiella phage RAN69Mutation(s): 0 
UniProt
Find proteins for A0AAE9HFU9 (Klebsiella phage FK1979)
Explore A0AAE9HFU9 
Go to UniProtKB:  A0AAE9HFU9
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UniProt GroupA0AAE9HFU9
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
gp20I [auth m],
J [auth g]
87Klebsiella phage RAN69Mutation(s): 0 
UniProt
Find proteins for A0A7D7F0N7 (Klebsiella virus KpV2883)
Explore A0A7D7F0N7 
Go to UniProtKB:  A0A7D7F0N7
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UniProt GroupA0A7D7F0N7
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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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