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- EMDB-2691: Inside rotavirus at 7 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-2691
TitleInside rotavirus at 7 A resolution
Map datalow-pass filtered map (10A) for dsRNA visualization
Sample
  • Sample: Rotavirus DLP+VP1
  • Protein or peptide: Rotavirus polymerase (VP1)
  • RNA: dsRNA
Keywordsrotavirus / dsRNA-dependent / polymerase / dsRNA / symmetry-mismatch / VP1
Biological speciesBovine rotavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2691.png

Downloads & links

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Map

FileDownload / File: emd_2691.map.gz / Format: CCP4 / Size: 23 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlow-pass filtered map (10A) for dsRNA visualization
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 184 pix.
= 365.08 Å		1.98 Å/pix.
x 183 pix.
= 363.096 Å		1.98 Å/pix.
x 183 pix.
= 363.096 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.98413 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.4 / Movie #1: 2
Minimum - Maximum-12.44486904 - 12.18700218
Average (Standard dev.)-0.00000698 (±0.92164183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-91-91-56
Dimensions183183184
Spacing183183184
CellA: 363.0958 Å / B: 363.0958 Å / C: 365.07993 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.9841311475411.9841311475411.9841304347826
M x/y/z183183184
origin x/y/z0.0000.0000.000
length x/y/z363.096363.096365.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-91-91-56
NC/NR/NS183183184
D min/max/mean-12.44512.187-0.000

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Supplemental data

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Sample components

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Entire : Rotavirus DLP+VP1

EntireName: Rotavirus DLP+VP1
Components
  • Sample: Rotavirus DLP+VP1
  • Protein or peptide: Rotavirus polymerase (VP1)
  • RNA: dsRNA

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Supramolecule #1000: Rotavirus DLP+VP1

SupramoleculeName: Rotavirus DLP+VP1 / type: sample / ID: 1000 / Oligomeric state: VP1 and dsRNA molecules / Number unique components: 2

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Macromolecule #1: Rotavirus polymerase (VP1)

MacromoleculeName: Rotavirus polymerase (VP1) / type: protein_or_peptide / ID: 1 / Name.synonym: 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
Source (natural)Organism: Bovine rotavirus / synonym: Rotavirus
Molecular weightTheoretical: 126.326 KDa

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Macromolecule #2: dsRNA

MacromoleculeName: dsRNA / type: rna / ID: 2 / Name.synonym: dsRNA / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Bovine rotavirus / synonym: Rotavirus

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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

Concentration5 mg/mL
BufferpH: 7.4
GridDetails: Lacy carbon and C-flat
VitrificationCryogen name: ETHANE / Chamber humidity: 30 % / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Home-made. Vitrification carried out in air at room temperature
Method: Blot for 3 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureAverage: 90 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected
DateJun 1, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 11289 / Average electron dose: 15 e/Å2 / Od range: 1 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 56540 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Eucentric, side-entry / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase-flipping
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: Imagic, RIco, bsoft, ctffind3, FPM / Number images used: 11289

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