9KYX | pdb_00009kyx

The scaffold tetramer of phage P22


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the scaffolding protein and portal within the bacteriophage P22 procapsid provides insights into the self-assembly process.

Xiao, H.Chen, W.Pang, H.Zheng, J.Wang, L.Feng, H.Song, J.Cheng, L.Liu, H.

(2025) PLoS Biol 23: e3003104-e3003104

  • DOI: https://doi.org/10.1371/journal.pbio.3003104
  • Primary Citation of Related Structures:  
    9JG6, 9JGA, 9KYV, 9KYW, 9KYX, 9KYY

  • PubMed Abstract: 

    In the assembly pathway of tailed double-stranded DNA (dsDNA) bacteriophages and herpesviruses, a procapsid with a dodecameric portal for DNA delivery at a unique vertex is initially formed. Appropriate procapsid assembly requires the transient presence of multiple copies of a scaffolding protein (SP), which is absent in the mature virion. However, how the SP contributes to dodecameric portal formation, facilitates portal and coat protein incorporation, and is subsequently released remains unclear because of a lack of structural information. Here, we present the structure of the SP-portal complex within the procapsid of bacteriophage P22 at 3-9 Å resolutions. The AlphaFold2-predicted SP model fits well with the density map of the complex. The SP forms trimers and tetramers that interact to yield a dome-like complex on the portal. Two SP domains mediate multimerization. Each trimer interacts with two neighboring portal subunits. The SP has a loop-hook-like structure that aids in coat protein recruitment during viral assembly. The loops of those SP subunits on the portal are positioned in clefts between adjacent portal subunits. Conformational changes in the portal during phage maturation may trigger the disassembly and release of the SP complex. Our findings provide insights into SP-assisted procapsid assembly in bacteriophage P22 and suggest that this strategy is also implemented by other dsDNA viruses, including herpesviruses.


  • Organizational Affiliation
    • Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Scaffolding protein
A, B, C, D, E
A, B, C, D, E, F, G, H
303Salmonella phage P22Mutation(s): 0 
UniProt
Find proteins for P26748 (Salmonella phage P22)
Explore P26748 
Go to UniProtKB:  P26748
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26748
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China12034006
National Natural Science Foundation of China (NSFC)China32430020
National Natural Science Foundation of China (NSFC)China32071209
National Natural Science Foundation of China (NSFC)China32371263
National Natural Science Foundation of China (NSFC)China32401014

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Database references