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- PDB-9c3b: Structure of the Shigella flexneri bacteriophage Sf14 - tail helical -

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Basic information

Entry
Database: PDB / ID: 9c3b
TitleStructure of the Shigella flexneri bacteriophage Sf14 - tail helical
Components
  • Putative structural protein
  • gp40
KeywordsVIRUS / Sf14
Function / homologyStructural protein ORF10, bacteriophage KPP10 / Protein of unknown function DUF3383 / Bacteriophage KPP10, Structural protein ORF10 / Protein of unknown function (DUF3383) / Uncharacterized protein / Putative structural protein
Function and homology information
Biological speciesShigella phage Sf14 (virus)
MethodELECTRON MICROSCOPY / helical 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: To Be Published
Title: Structure of the Shigella flexneri bacteriophage Sf14 tail baseplate
Authors: Subramanian, S. / Kerns, H.R. / Braverman, S.G. / Doore, S.M.
History
DepositionMay 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative structural protein
B: gp40


Theoretical massNumber of molelcules
Total (without water)65,0392
Polymers65,0392
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

#1: 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
#2: 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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical 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
VitrificationCryogen 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
Helical symmertyAngular rotation/subunit: 25.75 ° / Axial rise/subunit: 37.062 Å / Axial symmetry: C6
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23422 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0064423
ELECTRON MICROSCOPYf_angle_d0.6646030
ELECTRON MICROSCOPYf_dihedral_angle_d4.428625
ELECTRON MICROSCOPYf_chiral_restr0.044719
ELECTRON MICROSCOPYf_plane_restr0.005780

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