9C2D | pdb_00009c2d

Bacteriophage Sf14 Capsid Icosahedral reconstruction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

The structure of Shigella virus Sf14 reveals the presence of two decoration proteins and two long tail fibers.

Subramanian, S.Kerns, H.R.Braverman, S.G.Doore, S.M.

(2025) Commun Biol 8: 222-222

  • DOI: https://doi.org/10.1038/s42003-025-07668-x
  • Primary Citation of Related Structures:  
    9C2D, 9C39, 9C3A, 9C3B

  • PubMed Abstract: 

    Bacteriophage Sf14 infects the human pathogen Shigella flexneri. A previous low-resolution structure suggested the presence of a decoration protein on its T = 9 icosahedral capsid. Here, we determined high-resolution structures of the Sf14 capsid and neck, along with a moderate-resolution structure of the whole Sf14 tail and baseplate. These structures indicate the capsid has not one, but two different types of decoration proteins: a trimeric β-tulip lattice that covers the entire capsid and a set of Hoc-like proteins that bind preferentially to hexamers at the quasi-3-fold axes of symmetry. The neck also contains two sets of whiskers oriented in opposite directions, and the tail has two types of long tail fibers which may bind different receptors. Based on homology and phylogenetic analysis, Sf14 may be the product of multiple horizontal gene transfer events. The structures presented here can be used to investigate further hypotheses of phage structure-function relationships and structural diversity.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.

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
367Shigella phage Sf14Mutation(s): 0 
Gene Names: Sf14_gp34
UniProt
Find proteins for A0A2K9VK95 (Shigella phage Sf14)
Explore A0A2K9VK95 
Go to UniProtKB:  A0A2K9VK95
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K9VK95
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Structural protein
J, K, L, M, N
J, K, L, M, N, O, P, Q, R
125Shigella phage Sf14Mutation(s): 0 
Gene Names: Sf14_gp33
UniProt
Find proteins for A0A2K9VKC2 (Shigella phage Sf14)
Explore A0A2K9VKC2 
Go to UniProtKB:  A0A2K9VKC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K9VKC2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tail protein372Shigella phage Sf14Mutation(s): 0 
Gene Names: Sf14_gp20
UniProt
Find proteins for A0A2K9VK81 (Shigella phage Sf14)
Explore A0A2K9VK81 
Go to UniProtKB:  A0A2K9VK81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K9VK81
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI170608
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM116789

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Data collection, Database references