9C39 | pdb_00009c39

Bacteriophage Sf14 neck C6 reconstruction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein
A, B
488Shigella phage Sf14Mutation(s): 0 
Gene Names: Sf14_gp29
UniProt
Find proteins for A0A2K9VKD2 (Shigella phage Sf14)
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Go to UniProtKB:  A0A2K9VKD2
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UniProt GroupA0A2K9VKD2
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phage protein
C, D
149Shigella phage Sf14Mutation(s): 0 
Gene Names: Sf14_gp35
UniProt
Find proteins for A0A2K9VK88 (Shigella phage Sf14)
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UniProt GroupA0A2K9VK88
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Head-closure protein133Shigella phage Sf14Mutation(s): 0 
Gene Names: Sf14_gp37
UniProt
Find proteins for A0A2K9VK93 (Shigella phage Sf14)
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UniProt GroupA0A2K9VK93
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
gp119199Shigella phage Sf14Mutation(s): 0 
Gene Names: Sf14_gp38
UniProt
Find proteins for A0A2K9VK98 (Shigella phage Sf14)
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UniProt GroupA0A2K9VK98
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
gp40148Shigella phage Sf14Mutation(s): 0 
Gene Names: Sf14_gp40
UniProt
Find proteins for A0A2K9VK99 (Shigella phage Sf14)
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UniProt GroupA0A2K9VK99
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Putative structural protein450Shigella phage Sf14Mutation(s): 0 
Gene Names: Sf14_gp39
UniProt
Find proteins for A0A2K9VKE4 (Shigella phage Sf14)
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UniProt GroupA0A2K9VKE4
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
gp127
I, J
166Shigella phage Sf14Mutation(s): 0 
Gene Names: Sf14_gp30
UniProt
Find proteins for A0A2K9VK89 (Shigella phage Sf14)
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UniProt GroupA0A2K9VK89
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  • Reference Sequence
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Phage protein
K, L, M, N, O
K, L, M, N, O, P
110Shigella phage Sf14Mutation(s): 0 
Gene Names: Sf14_gp31
UniProt
Find proteins for A0A2K9VK97 (Shigella phage Sf14)
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UniProt GroupA0A2K9VK97
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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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