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- PDB-9c2d: Bacteriophage Sf14 Capsid Icosahedral reconstruction -

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Basic information

Entry
Database: PDB / ID: 9c2d
TitleBacteriophage Sf14 Capsid Icosahedral reconstruction
Components
  • Major capsid protein
  • Structural protein
  • Tail protein
KeywordsVIRUS / Sf14
Function / homology
Function and homology information


host cell cytoplasm
Similarity search - Function
Major capsid protein GpE / Phage major capsid protein E / : / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Major capsid protein GpE / Phage major capsid protein E / : / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Putative tail protein / Major capsid protein / Putative structural protein
Similarity search - Component
Biological speciesShigella phage Sf14 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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
Authors: Subramanian, S. / Kerns, H.R. / Braverman, S.G. / Doore, S.M.
History
DepositionMay 30, 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

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Structural protein
K: Structural protein
L: Structural protein
M: Structural protein
N: Structural protein
O: Structural protein
P: Structural protein
Q: Structural protein
R: Structural protein
S: Tail protein


Theoretical massNumber of molelcules
Total (without water)535,87019
Polymers535,87019
Non-polymers00
Water00
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Structural protein
K: Structural protein
L: Structural protein
M: Structural protein
N: Structural protein
O: Structural protein
P: Structural protein
Q: Structural protein
R: Structural protein
S: Tail protein
x 60


Theoretical massNumber of molelcules
Total (without water)32,152,1941140
Polymers32,152,1941140
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
Major capsid protein


Mass: 41595.992 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf14 (virus) / Gene: Sf14_gp34 / Production host: Shigella flexneri Y (bacteria) / References: UniProt: A0A2K9VK95
#2: Protein
Structural protein


Mass: 13574.381 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf14 (virus) / Gene: Sf14_gp33 / Production host: Shigella flexneri Y (bacteria) / References: UniProt: A0A2K9VKC2
#3: Protein Tail protein


Mass: 39336.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf14 (virus) / Gene: Sf14_gp20 / Production host: Shigella flexneri Y (bacteria) / References: UniProt: A0A2K9VK81
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 Sf14 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Shigella phage Sf14 (virus)
Source (recombinant)Organism: Shigella flexneri Y (bacteria)
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 software
IDNameVersionCategory
10cryoSPARC4.4.1initial Euler assignment
11cryoSPARC4.4.1final Euler assignment
13cryoSPARC4.4.13D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42269 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00336351
ELECTRON MICROSCOPYf_angle_d0.50349194
ELECTRON MICROSCOPYf_dihedral_angle_d4.0174916
ELECTRON MICROSCOPYf_chiral_restr0.0425465
ELECTRON MICROSCOPYf_plane_restr0.0046393

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