8H89

Capsid of Ralstonia phage GP4

  • Classification: VIRUS
  • Organism(s): Ralstonia phage GP4
  • Mutation(s): No 

  • Deposited: 2022-10-22 Released: 2022-11-16 
  • Deposition Author(s): Liu, H.R., Chen, W.Y.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A Capsid Structure of Ralstonia solanacearum podoviridae GP4 with a Triangulation Number T = 9.

Zheng, J.Chen, W.Xiao, H.Yang, F.Li, X.Song, J.Cheng, L.Liu, H.

(2022) Viruses 14

  • DOI: https://doi.org/10.3390/v14112431
  • Primary Citation of Related Structures:  
    8H89

  • PubMed Abstract: 

    GP4, a new Ralstonia solanacearum phage, is a short-tailed phage. Few structures of Ralstonia solanacearum phages have been resolved to near-atomic resolution until now. Here, we present a 3.7 Å resolution structure of the GP4 head by cryo-electron microscopy (cryo-EM). The GP4 head contains 540 copies of major capsid protein (MCP) gp2 and 540 copies of cement protein (CP) gp1 arranged in an icosahedral shell with a triangulation number T = 9. The structures of gp2 and gp1 show a canonical HK97-like fold and an Ig-like fold, respectively. The trimeric CPs stick on the surface of the head along the quasi-threefold axis of the icosahedron generating a sandwiched three-layer electrostatic complementary potential, thereby enhancing the head stability. The assembly pattern of the GP4 head provides a platform for the further exploration of the interaction between Ralstonia solanacearum and corresponding phages.


  • 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, Hunan Normal University, Changsha 410082, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I
369Ralstonia phage GP4Mutation(s): 0 
UniProt
Find proteins for A0A345GTT3 (Ralstonia phage GP4)
Explore A0A345GTT3 
Go to UniProtKB:  A0A345GTT3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A345GTT3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Virion associated protein
J, K, L, M, N
J, K, L, M, N, O, P, Q, R
157Ralstonia phage GP4Mutation(s): 0 
UniProt
Find proteins for A0A345GTT2 (Ralstonia phage GP4)
Explore A0A345GTT2 
Go to UniProtKB:  A0A345GTT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A345GTT2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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)China32071209
National Natural Science Foundation of China (NSFC)China32200994
National Natural Science Foundation of China (NSFC)China31971122

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2022-12-14
    Changes: Derived calculations
  • Version 1.3: 2023-04-19
    Changes: Database references
  • Version 1.4: 2023-08-30
    Changes: Data collection