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- PDB-9c39: Bacteriophage Sf14 neck C6 reconstruction -

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Basic information

Entry
Database: PDB / ID: 9c39
TitleBacteriophage Sf14 neck C6 reconstruction
Components
  • (Phage protein) x 2
  • Head-closure protein
  • Portal protein
  • Putative structural protein
  • gp119
  • gp127
  • gp40
KeywordsVIRUS / Sf14
Function / homology
Function and homology information


Phage neck terminator protein / Protein of unknown function DUF935 / Structural protein ORF10, bacteriophage KPP10 / Protein of unknown function DUF3383 / Portal protein of Mu bacteriophage / Bacteriophage KPP10, Structural protein ORF10 / Protein of unknown function (DUF3383)
Similarity search - Domain/homology
Phage protein / Uncharacterized protein / Head-closure protein / Phage protein / Uncharacterized protein / Uncharacterized protein / Putative portal protein / Putative structural protein
Similarity search - Component
Biological speciesShigella phage Sf14 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSubramanian, S. / Kerns, H.R. / Braverman, S.G. / Doore, S.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI170608 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116789 United States
CitationJournal: Commun Biol / Year: 2025
Title: The structure of Shigella virus Sf14 reveals the presence of two decoration proteins and two long tail fibers.
Authors: Sundharraman Subramanian / Hailey R Kerns / Samantha G Braverman / Sarah M Doore /
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 ...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.
History
DepositionMay 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Phage protein
D: Phage protein
E: Head-closure protein
F: gp119
G: gp40
H: Putative structural protein
I: gp127
J: gp127
K: Phage protein
L: Phage protein
M: Phage protein
N: Phage protein
O: Phage protein
P: Phage protein


Theoretical massNumber of molelcules
Total (without water)354,09716
Polymers354,09716
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 8 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein Portal protein


Mass: 55291.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf14 (virus) / Gene: Sf14_gp29 / Production host: Shigella flexneri Y (bacteria) / References: UniProt: A0A2K9VKD2
#2: Protein Phage protein


Mass: 17058.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf14 (virus) / Gene: Sf14_gp35 / Production host: Shigella flexneri Y (bacteria) / References: UniProt: A0A2K9VK88
#3: Protein Head-closure protein


Mass: 15467.466 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf14 (virus) / Gene: Sf14_gp37 / Production host: Shigella flexneri Y (bacteria) / References: UniProt: A0A2K9VK93
#4: Protein gp119


Mass: 22314.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf14 (virus) / Gene: Sf14_gp38 / Production host: Shigella flexneri Y (bacteria) / References: UniProt: A0A2K9VK98
#5: Protein gp40


Mass: 16204.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf14 (virus) / Gene: Sf14_gp40 / Production host: Shigella flexneri Y (bacteria) / References: UniProt: A0A2K9VK99
#6: Protein Putative structural protein


Mass: 48834.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf14 (virus) / Gene: Sf14_gp39 / Production host: Shigella flexneri Y (bacteria) / References: UniProt: A0A2K9VKE4
#7: Protein gp127


Mass: 18445.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf14 (virus) / Gene: Sf14_gp30 / Production host: Shigella flexneri Y (bacteria) / References: UniProt: A0A2K9VK89
#8: Protein
Phage protein


Mass: 11613.982 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf14 (virus) / Gene: Sf14_gp31 / Production host: Shigella flexneri Y (bacteria) / References: UniProt: A0A2K9VK97

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Shigella phage Sf14 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Shigella phage Sf14 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Shigella flexneri Y
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMtris(hydroxymethyl)aminomethaneTris1
210 mMmagnesium chlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 33 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37006 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00322812
ELECTRON MICROSCOPYf_angle_d0.67531035
ELECTRON MICROSCOPYf_dihedral_angle_d4.2253138
ELECTRON MICROSCOPYf_chiral_restr0.0443611
ELECTRON MICROSCOPYf_plane_restr0.0054009

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