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- EMDB-6272: Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstro... -

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Basic information

Entry
Database: EMDB / ID: EMD-6272
TitleSingle particle cryo-EM structure of rotavirus VP6 at 2.6 Angstroms resolution
Map dataUnsharpened reconstruction of rotavirus VP6
Sample
  • Sample: 13-fold average of VP6 trimer from full rotavirus reconstruction
  • Protein or peptide: Bovine rotavirus VP6
Keywordsrotavirus / VP6 / cryo-EM / single particle
Function / homology
Function and homology information


viral intermediate capsid / T=13 icosahedral viral capsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / metal ion binding
Similarity search - Function
Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Intermediate capsid protein VP6 / Intermediate capsid protein VP6
Similarity search - Component
Biological speciesBovine rotavirus strain UK/G6
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGrant T / Grigorieff N
CitationJournal: Elife / Year: 2015
Title: Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6.
Authors: Timothy Grant / Nikolaus Grigorieff /
Abstract: Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that ...Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that maximizes the signal-to-noise ratio in the image. Using a 2.6 Å resolution single particle cryo-EM reconstruction of rotavirus VP6, determined from movies recorded with a total exposure of 100 electrons/Å(2), we obtained accurate measurements of optimal exposure values over a wide range of resolutions. At low and intermediate resolutions, our measured values are considerably higher than obtained previously for crystalline specimens, indicating that both images and movies should be collected with higher exposures than are generally used. We demonstrate a method of using our optimal exposure values to filter movie frames, yielding images with improved contrast that lead to higher resolution reconstructions. This 'high-exposure' technique should benefit cryo-EM work on all types of samples, especially those of relatively low-molecular mass.
History
DepositionFeb 19, 2015-
Header (metadata) releaseMar 4, 2015-
Map releaseMar 4, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0198
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0198
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j9s
  • Surface level: 0.0198
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j9s
  • Surface level: 0.0198
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6272.png

emd_6272_1.png

Downloads & links

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Map

FileDownload / File: emd_6272.map.gz / Format: CCP4 / Size: 4.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened reconstruction of rotavirus VP6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 108 pix.
= 110.484 Å		1.02 Å/pix.
x 108 pix.
= 110.484 Å		1.02 Å/pix.
x 108 pix.
= 110.484 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.023 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0198 / Movie #1: 0.0198
Minimum - Maximum-0.01965467 - 0.04852662
Average (Standard dev.)0.00130357 (±0.00714011)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-54-54-54
Dimensions108108108
Spacing108108108
CellA=B=C: 110.484 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0231.0231.023
M x/y/z108108108
origin x/y/z0.0000.0000.000
length x/y/z110.484110.484110.484
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-54-54-54
NC/NR/NS108108108
D min/max/mean-0.0200.0490.001

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Supplemental data

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Sample components

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Entire : 13-fold average of VP6 trimer from full rotavirus reconstruction

EntireName: 13-fold average of VP6 trimer from full rotavirus reconstruction
Components
  • Sample: 13-fold average of VP6 trimer from full rotavirus reconstruction
  • Protein or peptide: Bovine rotavirus VP6

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Supramolecule #1000: 13-fold average of VP6 trimer from full rotavirus reconstruction

SupramoleculeName: 13-fold average of VP6 trimer from full rotavirus reconstruction
type: sample / ID: 1000 / Oligomeric state: Trimer / Number unique components: 1
Molecular weightTheoretical: 41 KDa

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Macromolecule #1: Bovine rotavirus VP6

MacromoleculeName: Bovine rotavirus VP6 / type: protein_or_peptide / ID: 1 / Name.synonym: Intermediate capsid protein VP6 / Number of copies: 3 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Bovine rotavirus strain UK/G6 / synonym: Rv a
Molecular weightTheoretical: 41 KDa
Recombinant expressionOrganism: Chlorocebus sabaeus (green monkey)
SequenceUniProtKB: Intermediate capsid protein VP6

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
GridDetails: C-Flat 1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK II / Method: Blot for 4-6 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Corrected at 29,000 times magnification
DateAug 13, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 531 / Average electron dose: 100 e/Å2
Details: 130-frame movies, 0.1 seconds per frame, 100e/A2 total dose. Super resolution.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 48876 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsAdditional 13-fold averaging was performed on top of the I symmetry.
CTF correctionDetails: Each Particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: OTHER / Software - Name: TIGRIS, IMAGIC, FREALIGN
Details: Final map is a 13-fold average of VP6 trimers from the asymmetric unit of the reconstruction of the whole capsid. Data at resolutions higher than 15A were not used for alignments.
Number images used: 4000

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Atomic model buiding 1

Initial modelPDB ID:

1qhd


Chain - Chain ID: A
SoftwareName: COOT
DetailsModel was refined by real space refinement using COOT and all restraints.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3j9s:
Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution

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