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- PDB-5vf3: Bacteriophage T4 isometric capsid -

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Basic information

Entry
Database: PDB / ID: 5vf3
TitleBacteriophage T4 isometric capsid
Components
  • (Highly immunogenic outer capsid protein) x 2
  • Capsid vertex protein gp24
  • Major capsid protein
  • Small outer capsid protein
KeywordsVIRUS / Bacteriophage T4 / isometric head / virus capsid assembly / triangulation numbers / size-determining mutations / capsid stabilization / capsid decoration proteins
Function / homology
Function and homology information


viral capsid, decoration / T=13 icosahedral viral capsid / viral capsid
Similarity search - Function
Small outer capsid protein Soc / Highly immunogenic outer capsid protein / Small outer capsid protein / Small outer capsid protein superfamily / Small outer capsid protein / Capsid vertex protein / Major capsid protein, Myoviridae / Major capsid protein Gp23 / Capsid protein, T4-like bacteriophage-like / PKD domain ...Small outer capsid protein Soc / Highly immunogenic outer capsid protein / Small outer capsid protein / Small outer capsid protein superfamily / Small outer capsid protein / Capsid vertex protein / Major capsid protein, Myoviridae / Major capsid protein Gp23 / Capsid protein, T4-like bacteriophage-like / PKD domain / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Outer Surface Protein A; domain 3 / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Small outer capsid protein / Major capsid protein / Highly immunogenic outer capsid protein / Capsid vertex protein
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen, Z. / Sun, L. / Zhang, Z. / Fokine, A. / Padilla-Sanchez, V. / Hanein, D. / Jiang, W. / Rossmann, M.G. / Rao, V.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
National Institutes of Health/Office of the DirectorS10 OD012372 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01 GM098412-S1 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses.
Authors: Zhenguo Chen / Lei Sun / Zhihong Zhang / Andrei Fokine / Victor Padilla-Sanchez / Dorit Hanein / Wen Jiang / Michael G Rossmann / Venigalla B Rao /
Abstract: The 3.3-Å cryo-EM structure of the 860-Å-diameter isometric mutant bacteriophage T4 capsid has been determined. WT T4 has a prolate capsid characterized by triangulation numbers (T numbers) T = 13 ...The 3.3-Å cryo-EM structure of the 860-Å-diameter isometric mutant bacteriophage T4 capsid has been determined. WT T4 has a prolate capsid characterized by triangulation numbers (T numbers) T = 13 for end caps and T = 20 for midsection. A mutation in the major capsid protein, gp23, produced T=13 icosahedral capsids. The capsid is stabilized by 660 copies of the outer capsid protein, Soc, which clamp adjacent gp23 hexamers. The occupancies of Soc molecules are proportional to the size of the angle between the planes of adjacent hexameric capsomers. The angle between adjacent hexameric capsomers is greatest around the fivefold vertices, where there is the largest deviation from a planar hexagonal array. Thus, the Soc molecules reinforce the structure where there is the greatest strain in the gp23 hexagonal lattice. Mutations that change the angles between adjacent capsomers affect the positions of the pentameric vertices, resulting in different triangulation numbers in bacteriophage T4. The analysis of the T4 mutant head assembly gives guidance to how other icosahedral viruses reproducibly assemble into capsids with a predetermined T number, although the influence of scaffolding proteins is also important.
History
DepositionApr 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-8661
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-8661
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
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Assembly

Deposited unit
a: Capsid vertex protein gp24
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: Major capsid protein
K: Major capsid protein
L: Major capsid protein
O: Small outer capsid protein
P: Small outer capsid protein
Q: Small outer capsid protein
R: Small outer capsid protein
S: Small outer capsid protein
T: Small outer capsid protein
U: Small outer capsid protein
V: Small outer capsid protein
W: Small outer capsid protein
X: Small outer capsid protein
Y: Small outer capsid protein
Z: Highly immunogenic outer capsid protein
z: Highly immunogenic outer capsid protein


Theoretical massNumber of molelcules
Total (without water)772,23226
Polymers772,23226
Non-polymers00
Water0
1
a: Capsid vertex protein gp24
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: Major capsid protein
K: Major capsid protein
L: Major capsid protein
O: Small outer capsid protein
P: Small outer capsid protein
Q: Small outer capsid protein
R: Small outer capsid protein
S: Small outer capsid protein
T: Small outer capsid protein
U: Small outer capsid protein
V: Small outer capsid protein
W: Small outer capsid protein
X: Small outer capsid protein
Y: Small outer capsid protein
Z: Highly immunogenic outer capsid protein
z: Highly immunogenic outer capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)46,333,9271560
Polymers46,333,9271560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
a: Capsid vertex protein gp24
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: Major capsid protein
K: Major capsid protein
L: Major capsid protein
O: Small outer capsid protein
P: Small outer capsid protein
Q: Small outer capsid protein
R: Small outer capsid protein
S: Small outer capsid protein
T: Small outer capsid protein
U: Small outer capsid protein
V: Small outer capsid protein
W: Small outer capsid protein
X: Small outer capsid protein
Y: Small outer capsid protein
Z: Highly immunogenic outer capsid protein
z: Highly immunogenic outer capsid protein
x 5


  • icosahedral pentamer
  • 3.86 MDa, 130 polymers
Theoretical massNumber of molelcules
Total (without water)3,861,161130
Polymers3,861,161130
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
a: Capsid vertex protein gp24
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: Major capsid protein
K: Major capsid protein
L: Major capsid protein
O: Small outer capsid protein
P: Small outer capsid protein
Q: Small outer capsid protein
R: Small outer capsid protein
S: Small outer capsid protein
T: Small outer capsid protein
U: Small outer capsid protein
V: Small outer capsid protein
W: Small outer capsid protein
X: Small outer capsid protein
Y: Small outer capsid protein
Z: Highly immunogenic outer capsid protein
z: Highly immunogenic outer capsid protein
x 6


  • icosahedral 23 hexamer
  • 4.63 MDa, 156 polymers
Theoretical massNumber of molelcules
Total (without water)4,633,393156
Polymers4,633,393156
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid vertex protein gp24 / Gene product 24 / gp24 / gp24*


Mass: 45838.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / References: UniProt: P19896
#2: Protein
Major capsid protein / Gene product 23 / gp23 / Major head protein / gp23*


Mass: 48728.863 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / References: UniProt: P04535
#3: Protein
Small outer capsid protein / Soc


Mass: 9085.095 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / References: UniProt: P03715
#4: Protein Highly immunogenic outer capsid protein / Hoc


Mass: 40416.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / References: UniProt: P18056
#5: Protein/peptide Highly immunogenic outer capsid protein / Hoc


Mass: 1294.587 Da / Num. of mol.: 1 / Fragment: unidentified segment / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Enterobacteria phage T4 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Enterobacteria phage T4 (virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Escherichia coli
Virus shellName: gp23*-gp24*-Soc-Hoc / Diameter: 860 nm / Triangulation number (T number): 13
Buffer solutionpH: 7
Details: 50 mM sodium phosphate, pH 7.0, 75 mM sodium chloride, 1 mM magnesium chloride
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: High-purity sample, volume = 50 uL, 10^12 particles
Specimen supportDetails: glow discharge for 60 seconds with 30 mA current / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Ted Pella
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 298 K / Details: Blot for 8 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Data collection by Leginon
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 18000 X / Calibrated magnification: 18000 X / Nominal defocus max: -3000 nm / Nominal defocus min: -1000 nm / Calibrated defocus min: -800 nm / Calibrated defocus max: -3500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER / Temperature (max): 100 K / Temperature (min): 90 K / Residual tilt: 0.5 mradians
Image recordingAverage exposure time: 9 sec. / Electron dose: 26 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3000
Details: Images were collected in super-resolution mode at 40 frames per second.
Image scansSampling size: 2 µm / Width: 3710 / Height: 3838 / Movie frames/image: 75 / Used frames/image: 3-22

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Processing

EM software
IDNameCategory
7Cootmodel fitting
9PHENIXmodel refinement
11EMAN, JSPRfinal Euler assignment
12RELIONclassification
Image processingDetails: The selected images were gain-normalized.
CTF correctionDetails: CTF amplitude correction was performed during 3D reconstruction.
Type: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 19000
Details: Approximately 1000 manually-picked particles were used for 2D classification. Templates were then generated from these 2D classes and used for automated particle picking.
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18000 / Algorithm: FOURIER SPACE
Details: Independent refinement of even/odd map, gold standard
Num. of class averages: 60 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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