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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
DescriptorCapsid vertex protein gp24
Major capsid protein
Small outer capsid protein
Highly immunogenic outer capsid protein
KeywordsVIRUS / Bacteriophage T4 / isometric head / virus capsid assembly / triangulation numbers / size-determining mutations / capsid stabilization / capsid decoration proteins
Specimen sourceEnterobacteria phage T4 / virus
MethodElectron microscopy (3.3 Å resolution / 2d array / Single particle)
AuthorsChen, Z. / Sun, L. / Zhang, Z. / Fokine, A. / Padilla-Sanchez, V. / Hanein, D. / Jiang, W. / Rossmann, M.G. / Rao, V.B.
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, E8184-E8193

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E8184-E8193 Yorodumi Papers
Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses.
Zhenguo Chen / Lei Sun / Zhihong Zhang / Andrei Fokine / Victor Padilla-Sanchez / Dorit Hanein / Wen Jiang / Michael G Rossmann / Venigalla B Rao

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 6, 2017 / Release: Sep 13, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 13, 2017Structure modelrepositoryInitial release
1.1Sep 27, 2017Structure modelAuthor supporting evidence / Database referencescitation / pdbx_audit_support_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
1.2Oct 11, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-8661
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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
Polyers772,23226
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
Polyers46,333,9271560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#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
Polyers3,861,161130
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#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
Polyers4,633,393156
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
#5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Polypeptide(L)Capsid vertex protein gp24 / Gene product 24 / gp24 / gp24*


Mass: 45838.574 Da / Num. of mol.: 1 / Source: (natural) Enterobacteria phage T4 / virus / References: UniProt: P19896

Cellular component

#2: Polypeptide(L)
Major capsid protein / Gene product 23 / gp23 / Major head protein / gp23*


Mass: 48728.863 Da / Num. of mol.: 12 / Source: (natural) Enterobacteria phage T4 / virus / References: UniProt: P04535

Cellular component

#3: Polypeptide(L)
Small outer capsid protein / Soc


Mass: 9085.095 Da / Num. of mol.: 11 / Source: (natural) Enterobacteria phage T4 / virus / References: UniProt: P03715

Cellular component

#4: Polypeptide(L)Highly immunogenic outer capsid protein / Hoc


Mass: 40416.547 Da / Num. of mol.: 1 / Source: (natural) Enterobacteria phage T4 / virus / References: UniProt: P18056

Cellular component

#5: Polypeptide(L)Highly immunogenic outer capsid protein / Hoc


Mass: 1294.587 Da / Num. of mol.: 1 / Fragment: unidentified segment / 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 / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Enterobacteria phage T4 / Type: VIRUS / Entity ID: 1,2,3,4,5 / Source: NATURAL
Source (natural)Organism: Enterobacteria phage T4
Details of virusEmpty: YES / Enveloped: NO / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Escherichia coli
Virus shellName: gp23*-gp24*-Soc-Hoc / Diameter: 860 Å / Triangulation number (T number): 13
Buffer solutionDetails: 50 mM sodium phosphate, pH 7.0, 75 mM sodium chloride, 1 mM magnesium chloride
pH: 7
SpecimenConc.: 1 mg/ml
Details: High-purity sample, volume = 50 uL, 10^12 particles
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow discharge for 60 seconds with 30 mA current / Grid material: COPPER / Grid mesh size: 400 / Grid type: Ted Pella
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 298 kelvins / Details: Blot for 8 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 FIELD / Nominal magnification: 18000 / Calibrated magnification: 18000 / 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 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER / Temperature (max): 100 kelvins / Temperature (min): 90 kelvins / Residual tilt: 0.5 mradians
Image recordingAverage exposure time: 9 sec. / Electron dose: 26 e/Å2
Details: Images were collected in super-resolution mode at 40 frames per second.
Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 3000
Image scansSampling size: 2 microns / Dimension width: 3710 / Dimension height: 3838 / Movie frames/image: 75 / Used frames/image: 3-22

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Processing

EM software
IDNameCategoryFitting IDImage processing ID
7CootMODEL FITTING1
9phenix.real_space_refineMODEL REFINEMENT1
11EMAN, JSPRFINAL EULER ASSIGNMENT1
12RELIONCLASSIFICATION1
Image processingDetails: The selected images were gain-normalized.
CTF correctionDetails: CTF amplitude correction was performed during 3D reconstruction.
Type: PHASE FLIPPING ONLY
Particle selectionDetails: Approximately 1000 manually-picked particles were used for 2D classification. Templates were then generated from these 2D classes and used for automated particle picking.
Number of particles selected: 19000
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 18000 / Algorithm: FOURIER SPACE
Details: Independent refinement of even/odd map, gold standard
Number of class averages: 60 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL

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