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- EMDB-8661: Cryo-EM reconstruction of the bacteriophage T4 isometric capsid -

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Basic information

Entry
Database: EMDB / ID: 8661
TitleCryo-EM reconstruction of the bacteriophage T4 isometric capsid
Map dataCryo-EM reconstruction of the bacteriophage T4 isometric capsid
SampleEnterobacteria phage T4
  • virus
  • Capsid vertex protein gp24
  • Major capsid protein
  • Small outer capsid protein
  • (Highly immunogenic outer capsid ...) x 2
Function / homologyImmunoglobulin-like domain superfamily / Small outer capsid protein / Capsid vertex protein / Highly immunogenic outer capsid protein / Major capsid protein, Myoviridae / Small outer capsid protein superfamily / Small outer capsid protein / PKD domain superfamily / PKD/Chitinase domain / Major capsid protein Gp23 ...Immunoglobulin-like domain superfamily / Small outer capsid protein / Capsid vertex protein / Highly immunogenic outer capsid protein / Major capsid protein, Myoviridae / Small outer capsid protein superfamily / Small outer capsid protein / PKD domain superfamily / PKD/Chitinase domain / Major capsid protein Gp23 / Immunoglobulin-like fold / Capsid protein, T4-like bacteriophage-like / Immunoglobulin-like domain / PKD domain / PKD domain / viral capsid, decoration / T=13 icosahedral viral capsid / virion / viral capsid / Small outer capsid protein / Major capsid protein / Highly immunogenic outer capsid protein / Capsid vertex protein
Function and homology information
SourceEnterobacteria phage T4 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsChen Z / Sun L
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
Validation ReportPDB-ID: 5vf3

SummaryFull reportAbout validation report
DateDeposition: Apr 6, 2017 / Header (metadata) release: Jul 19, 2017 / Map release: Sep 13, 2017 / Last update: Oct 11, 2017

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Structure visualization

Movie
  • Colored surface
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5vf3
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5vf3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8661.map.gz (map file in CCP4 format, 1610613 KB)
Voxel sizeX=Y=Z: 0.81 Å
Density
Contour Level:8 (by emdb), 4 (movie #1):
Minimum - Maximum-31.03254 - 42.34649
Average (Standard dev.)0.005835759 (1.7083335)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions153615361536
Origin-768-768-768
Limit767767767
Spacing153615361536
CellA=B=C: 1244.16 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z153615361536
origin x/y/z0.0000.0000.000
length x/y/z1244.1601244.1601244.160
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-768-768-768
NC/NR/NS153615361536
D min/max/mean-31.03342.3460.006

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Supplemental data

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Sample components

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Entire Enterobacteria phage T4

EntireName: Enterobacteria phage T4 / Number of components: 6

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Component #1: virus, Enterobacteria phage T4

VirusName: Enterobacteria phage T4 / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Enterobacteria phage T4 (bacteriophage)
Source (natural)Host Species: Escherichia coli (E. coli)
Shell #1Name of element: gp23*-gp24*-Soc-Hoc / Diameter: 860 Å / T number(triangulation number): 13

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Component #2: protein, Capsid vertex protein gp24

ProteinName: Capsid vertex protein gp24 / Recombinant expression: No
MassTheoretical: 45.838574 kDa
SourceSpecies: Enterobacteria phage T4 (bacteriophage)

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Component #3: protein, Major capsid protein

ProteinName: Major capsid protein / Recombinant expression: No
MassTheoretical: 48.728863 kDa
SourceSpecies: Enterobacteria phage T4 (bacteriophage)

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Component #4: protein, Small outer capsid protein

ProteinName: Small outer capsid protein / Recombinant expression: No
MassTheoretical: 9.085095 kDa
SourceSpecies: Enterobacteria phage T4 (bacteriophage)

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Component #5: protein, Highly immunogenic outer capsid protein

ProteinName: Highly immunogenic outer capsid protein / Recombinant expression: No
MassTheoretical: 40.416547 kDa
SourceSpecies: Enterobacteria phage T4 (bacteriophage)

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Component #6: protein, Highly immunogenic outer capsid protein

ProteinName: Highly immunogenic outer capsid protein / Recombinant expression: No
MassTheoretical: 1.294587 kDa
SourceSpecies: Enterobacteria phage T4 (bacteriophage)

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Experimental details

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Sample preparation

SpecimenSpecimen state: 2D array / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 50 mM sodium phosphate, pH 7.0, 75 mM sodium chloride, 1 mM magnesium chloride
pH: 7
Support filmglow discharge for 60 seconds with 30 mA current
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 80 % / Details: Blot for 8 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Data collection by Leginon
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 26 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 18000 X (nominal), 18000 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1000 - -3000 nm
Specimen HolderModel: OTHER / Temperature: K ( 90 - 100 K)
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3000 / Sampling size: 2 microns
Details: Images were collected in super-resolution mode at 40 frames per second.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 18000 / Details: The selected images were gain-normalized.
3D reconstructionAlgorithm: FOURIER SPACE
CTF correction: CTF amplitude correction was performed during 3D reconstruction.
Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Independent refinement of even/odd map, gold standard
Euler angles: EMAN and JSPR were used for refinement.

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Atomic model buiding

Output model

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