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- EMDB-8251: Subtomogram-averaged map of in vitro assembled rubella virus caps... -

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Basic information

Entry
Database: EMDB / ID: 8251
TitleSubtomogram-averaged map of in vitro assembled rubella virus capsid protein tetramer complex
SampleRubella virus capsid protein
SourceRubella virus strain M33 / virus
Map dataSubtomogram-averaged map of in vitro assembled rubella virus capsid protein tetramer complex, unfiltered and unmasked
Methodsubtomogram averaging, at 35 Å resolution
AuthorsMangala Prasad V / Klose T / Rossmann MG
CitationPLoS Pathog., 2017, 13, e1006377-e1006377

PLoS Pathog., 2017, 13, e1006377-e1006377 StrPapers
Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.
Vidya Mangala Prasad / Thomas Klose / Michael G Rossmann

DateDeposition: Jun 14, 2016 / Header (metadata) release: Jul 13, 2016 / Map release: May 10, 2017 / Last update: Jun 14, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8251.map.gz (map file in CCP4 format, 501 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
50 pix
5.28 Å/pix.
= 264. Å
50 pix
5.28 Å/pix.
= 264. Å
50 pix
5.28 Å/pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 5.28 Å
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-4.8632483 - 6.4853272
Average (Standard dev.)-3.9384766E-8 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions505050
Origin-25-25-25
Limit242424
Spacing505050
CellA=B=C: 264 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.285.285.28
M x/y/z505050
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-25-25-25
NC/NR/NS505050
D min/max/mean-4.8636.485-0.000

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Supplemental data

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Sample components

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Entire Rubella virus capsid protein

EntireName: Rubella virus capsid protein / Number of components: 2
MassExperimental: 256 kDa

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Component #1: protein, Rubella virus capsid protein

ProteinName: Rubella virus capsid protein / Recombinant expression: No
MassExperimental: 256 kDa
SourceSpecies: Rubella virus strain M33 / virus
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli
Vector: pTXB1 / Strain: Rosetta-2 (DE3)

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Component #2: protein, Rubella virus capsid protein

ProteinName: Rubella virus capsid protein / Recombinant expression: No
Source (engineered)Expression System: Rubella virus strain M33 / virus

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 90 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 11000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: - 5 nm
Specimen HolderModel: OTHER / Tilt Angle: -60 - 60 deg.
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionSoftware: PEET / Resolution: 35 Å / Resolution method: OTHER

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