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- PDB-9occ: Sf11 bacteriophage tail -

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Basic information

Entry
Database: PDB / ID: 9occ
TitleSf11 bacteriophage tail
Components
  • (Putative tail protein ...) x 2
  • Putative neck whiskers protein gp24
  • Tail fiber protein gp17
  • Tail tape measure protein gp18
  • gp16
KeywordsVIRUS / Sf11 / bacteriophage
Function / homology
Function and homology information


viral tail assembly
Similarity search - Function
Tape measure protein N-terminal / Tape measure protein / Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Putative tail protein / Tail tape measure protein / Tail fiber protein / Putative neck whiskers protein / Putative tail protein / Uncharacterized protein
Similarity search - Component
Biological speciesShigella phage Sf11 SMD-2017 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSubramanian, S. / Parent, K.N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140803 United States
National Science Foundation (NSF, United States)1750125 United States
CitationJournal: To Be Published
Title: Structure of Shigella bacteriophage Sf11
Authors: Subramanian, S. / Dover, J.A. / Parent, K.N.
History
DepositionApr 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative neck whiskers protein gp24
B: Putative neck whiskers protein gp24
C: Tail fiber protein gp17
D: Tail fiber protein gp17
E: Putative tail protein gp14
F: gp16
G: Putative tail protein gp13
H: Putative tail protein gp13
I: Putative tail protein gp13
J: Putative tail protein gp13
K: Putative tail protein gp13
L: Putative tail protein gp13
M: Tail tape measure protein gp18


Theoretical massNumber of molelcules
Total (without water)714,50613
Polymers714,50613
Non-polymers00
Water00
1
A: Putative neck whiskers protein gp24
B: Putative neck whiskers protein gp24
C: Tail fiber protein gp17
D: Tail fiber protein gp17
E: Putative tail protein gp14
F: gp16
G: Putative tail protein gp13
H: Putative tail protein gp13
I: Putative tail protein gp13
J: Putative tail protein gp13
K: Putative tail protein gp13
L: Putative tail protein gp13
M: Tail tape measure protein gp18

A: Putative neck whiskers protein gp24
B: Putative neck whiskers protein gp24
C: Tail fiber protein gp17
D: Tail fiber protein gp17
E: Putative tail protein gp14
F: gp16
G: Putative tail protein gp13
H: Putative tail protein gp13
I: Putative tail protein gp13
J: Putative tail protein gp13
K: Putative tail protein gp13
L: Putative tail protein gp13
M: Tail tape measure protein gp18

A: Putative neck whiskers protein gp24
B: Putative neck whiskers protein gp24
C: Tail fiber protein gp17
D: Tail fiber protein gp17
E: Putative tail protein gp14
F: gp16
G: Putative tail protein gp13
H: Putative tail protein gp13
I: Putative tail protein gp13
J: Putative tail protein gp13
K: Putative tail protein gp13
L: Putative tail protein gp13
M: Tail tape measure protein gp18

A: Putative neck whiskers protein gp24
B: Putative neck whiskers protein gp24
C: Tail fiber protein gp17
D: Tail fiber protein gp17
E: Putative tail protein gp14
F: gp16
G: Putative tail protein gp13
H: Putative tail protein gp13
I: Putative tail protein gp13
J: Putative tail protein gp13
K: Putative tail protein gp13
L: Putative tail protein gp13
M: Tail tape measure protein gp18


Theoretical massNumber of molelcules
Total (without water)2,858,02552
Polymers2,858,02552
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1_555x,y,z1
point symmetry operation2
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))

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Components

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Protein , 4 types, 6 molecules ABCDFM

#1: Protein Putative neck whiskers protein gp24


Mass: 25037.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf11 SMD-2017 (virus) / References: UniProt: A0A291AXD7
#2: Protein Tail fiber protein gp17


Mass: 50176.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf11 SMD-2017 (virus) / References: UniProt: A0A291AXC9
#4: Protein gp16


Mass: 17654.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf11 SMD-2017 (virus) / References: UniProt: A0A291AXG1
#6: Protein Tail tape measure protein gp18


Mass: 82248.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf11 SMD-2017 (virus) / References: UniProt: A0A291AXC6

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Putative tail protein ... , 2 types, 7 molecules EGHIJKL

#3: Protein Putative tail protein gp14


Mass: 92301.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf11 SMD-2017 (virus) / References: UniProt: A0A291AXC5
#5: Protein
Putative tail protein gp13


Mass: 61978.992 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf11 SMD-2017 (virus) / References: UniProt: A0A291AXF7

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Details

Has protein modificationN

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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 Sf11 SMD-2017 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Shigella phage Sf11 SMD-2017 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Shigella flexneri Y
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
110 mMtris(hydroxymethyl)aminomethane1
210 mMmagnesium chloride1
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50.45 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35748 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00615328
ELECTRON MICROSCOPYf_angle_d0.60720865
ELECTRON MICROSCOPYf_dihedral_angle_d4.7392059
ELECTRON MICROSCOPYf_chiral_restr0.0452329
ELECTRON MICROSCOPYf_plane_restr0.0052709

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