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- EMDB-2690: Inside rotavirus at 7 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-2690
TitleInside rotavirus at 7 A resolution
Map data
SampleRotavirus DLP+VP1:
Rotavirus polymerase (VP1) / nucleic-acidNucleic acid
Keywordsrotavirus / symmetry-mismatch / RdRp / VP1 / dsRNA / transcription / replication.
Biological speciesBovine rotavirus (Rotavirus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsEstrozi LF
CitationJournal: To Be Published
Title: Inside rotavirus at 7 A resolution
Authors: Estrozi LF
History
DepositionJun 23, 2014-
Header (metadata) releaseJul 30, 2014-
Map releaseJul 15, 2015-
UpdateJul 15, 2015-
Current statusJul 15, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_2690.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 125 pix.
= 248.016 Å
1.98 Å/pix.
x 125 pix.
= 248.016 Å
1.98 Å/pix.
x 125 pix.
= 248.016 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.98413 Å
Density
Contour LevelBy EMDB: 0.4 / Movie #1: 2
Minimum - Maximum-10.62330818 - 17.37676811
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-62-62-62
Dimensions125125125
Spacing125125125
CellA=B=C: 248.01625 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.9841281.9841281.984128
M x/y/z125125125
origin x/y/z0.0000.0000.000
length x/y/z248.016248.016248.016
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-62-62-62
NC/NR/NS125125125
D min/max/mean-10.62317.377-0.000

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Supplemental data

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Sample components

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Entire Rotavirus DLP+VP1

EntireName: Rotavirus DLP+VP1 / Number of components: 2 / Oligomeric State: VP1 and dsRNA molecules

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Component #1: protein, Rotavirus polymerase (VP1)

ProteinName: Rotavirus polymerase (VP1) / a.k.a: VP1
Details: The icosahedral 3D reconstruction of rotavirus DLP shows extra-density near the 5-fold axis corresponding to one copy of VP1 attached to the DLP inner surface.
Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 126.326 kDa
SourceSpecies: Bovine rotavirus (Rotavirus)

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Component #2: nucleic-acid, dsRNA

nucleic acidName: dsRNARNA / a.k.a: dsRNARNA / Class: RNA / Structure: DOUBLE HELIX / Synthetic: No
SourceSpecies: Bovine rotavirus (Rotavirus)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/mL / pH: 7.4
Support filmLacy carbon and C-flat
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 30 % / Method: Blot for 3 seconds before plunging
Details: Vitrification instrument: Home-made. Vitrification carried out in air at room temperature

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30 / Date: Jun 1, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 56540 X (calibrated) / Astigmatism: Objective lens astigmatism was corrected / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1100 - 3500 nm
Specimen HolderHolder: Eucentric, side-entry / Model: GATAN LIQUID NITROGEN / Temperature: 90
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 11289 / Scanner: ZEISS SCAI / Sampling size: 7 µm / Bit depth: 8 / OD range: 1
URL of raw data: http://grigoriefflab.janelia.org/rotavirusdlp

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 11289
3D reconstructionAlgorithm: Symmetry adapted functions with symmetry-mismatch method
Software: Imagic, RIco, bsoft, ctffind3, FPM / CTF correction: Phase-flipping / Resolution: 7 Å / Resolution method: FSC 0.143, semi-independent

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Atomic model buiding

Modeling #1Software: VEDA / Refinement protocol: rigid body / Target criteria: CC / Refinement space: RECIPROCAL
Input PDB model: 2R7W
Chain ID: A

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