9VEL | pdb_00009vel

The composite cryo-EM structure of bacteriophage SPO1 capsid


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Capsid structure of phage SPO1 reveals novel minor capsid proteins and insights into capsid stabilization.

Zhao, X.Wang, A.Wang, Y.Kang, Y.Shao, Q.Li, L.Zheng, Y.Hu, H.Li, X.Fan, H.Cai, C.Liu, B.Fang, Q.

(2025) Structure 33: 1844

  • DOI: https://doi.org/10.1016/j.str.2025.08.004
  • Primary Citation of Related Structures:  
    9VEL

  • PubMed Abstract: 

    SPO1-related bacteriophages are promising candidates for phage therapy. We present the 3.0 Å cryo-electron microscopy (cryo-EM) structure of the SPO1 capsid with a triangulation number T = 16, enabling the construction of an atomic model comprising the major capsid protein and three types of minor capsid proteins: gp29.2, gp2.7, and gp36.3. These minor capsid proteins adopt novel folds. They might stabilize the capsid and determine its curvature. Gp29.2 monomers contain a three-blade propeller fold and are located at the 3-fold and quasi-three-fold axes. Gp2.7 forms pentamers atop pentameric capsomers, while gp36.3 binds to the capsid's inner surface, forming star-shaped structures increasing connections between pentameric and hexameric capsomers. The surface exposed regions of gp29.2 and gp2.7 make SPO1 of interest as a nanocage for phage display. Our findings advance the understanding of capsid architecture, stabilization, and local curvature determination for SPO1-related bacteriophages.


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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gp6.1468Bacillus phage SPO1Mutation(s): 0 
UniProt
Find proteins for B6V2N7 (Bacillus phage SP01)
Explore B6V2N7 
Go to UniProtKB:  B6V2N7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6V2N7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gp29.2N [auth r],
O [auth q],
P [auth s],
U [auth v]
171Bacillus phage SPO1Mutation(s): 0 
UniProt
Find proteins for B6V2J1 (Bacillus phage SP01)
Explore B6V2J1 
Go to UniProtKB:  B6V2J1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6V2J1
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gp2.7T [auth t]57Bacillus phage SPO1Mutation(s): 0 
UniProt
Find proteins for B6V2M7 (Bacillus phage SP01)
Explore B6V2M7 
Go to UniProtKB:  B6V2M7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6V2M7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Gp36.3V [auth w]96Bacillus phage SPO1Mutation(s): 0 
UniProt
Find proteins for B6V2H5 (Bacillus phage SP01)
Explore B6V2H5 
Go to UniProtKB:  B6V2H5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6V2H5
Sequence Annotations
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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 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Data collection, Database references
  • Version 1.2: 2025-11-26
    Changes: Data collection, Database references