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- EMDB-8249: Subtomogram-averaged map of a single rubella virus capsid unit -

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Basic information

Database: EMDB / ID: 8249
TitleSubtomogram-averaged map of a single rubella virus capsid unit
SampleRubella virus strain M33
SourceRubella virus strain M33 / virus
Map dataSubtomogram-averaged single capsid unit
Methodsubtomogram averaging, at 35 Å resolution
AuthorsMangala Prasad V / Klose T
CitationPLoS Pathog., 2017, 13, e1006377-e1006377

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

Validation ReportPDB-ID: 5khe

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

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 1.95
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 1.95
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5khe
  • Surface level: 1.95
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_8249.map.gz (map file in CCP4 format, 56 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
24 pix
5.28 Å/pix.
= 126.72 Å
24 pix
5.28 Å/pix.
= 126.72 Å
24 pix
5.28 Å/pix.
= 126.72 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 5.28 Å
Contour Level:1.95 (by author), 1.95 (movie #1):
Minimum - Maximum-3.2933166 - 4.881808
Average (Standard dev.)0.2174404 (0.88683295)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 126.72 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.285.285.28
M x/y/z242424
origin x/y/z0.0000.0000.000
length x/y/z126.720126.720126.720
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-12-12-12
D min/max/mean-3.2934.8820.217

Supplemental data

Sample components

Entire Rubella virus strain M33

EntireName: Rubella virus strain M33 / Number of components: 3
MassTheoretical: 64 kDa

Component #1: protein, Rubella virus strain M33

ProteinName: Rubella virus strain M33 / Recombinant expression: No
MassTheoretical: 64 kDa
SourceSpecies: Rubella virus strain M33 / virus
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli
Vector: pTXB1 / Strain: BL21(DE3)

Component #2: protein, capsid protein

ProteinName: capsid protein / Recombinant expression: No
MassTheoretical: 30.016332 kDa
Source (engineered)Expression System: Rubella virus / virus / 風疹ウイルス

Component #3: ligand, water

LigandName: water / Number of Copies: 35 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.2
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE

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: 1 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 11000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 500 - nm
Specimen HolderModel: OTHER / Tilt Angle: -60 - 60 deg.
CameraDetector: GATAN K2 (4k x 4k)

Image processing

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

Atomic model buiding

Output model

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