+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2691 | |||||||||
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Title | Inside rotavirus at 7 A resolution | |||||||||
Map data | low-pass filtered map (10A) for dsRNA visualization | |||||||||
Sample |
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Keywords | rotavirus / dsRNA-dependent / polymerase / dsRNA / symmetry-mismatch / VP1 | |||||||||
Biological species | Bovine rotavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.0 Å | |||||||||
Authors | Estrozi LF | |||||||||
Citation | Journal: To Be Published Title: Inside rotavirus at 7 A resolution Authors: Estrozi LF | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2691.map.gz | 3.8 MB | EMDB map data format | |
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Header (meta data) | emd-2691-v30.xml emd-2691.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | EMD-2691.png | 265.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2691 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2691 | HTTPS FTP |
-Validation report
Summary document | emd_2691_validation.pdf.gz | 211.4 KB | Display | EMDB validaton report |
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Full document | emd_2691_full_validation.pdf.gz | 210.5 KB | Display | |
Data in XML | emd_2691_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2691 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2691 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2691.map.gz / Format: CCP4 / Size: 23 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | low-pass filtered map (10A) for dsRNA visualization | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.98413 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Rotavirus DLP+VP1
Entire | Name: Rotavirus DLP+VP1 |
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Components |
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-Supramolecule #1000: Rotavirus DLP+VP1
Supramolecule | Name: 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)
Macromolecule | Name: 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 |
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Source (natural) | Organism: Bovine rotavirus / synonym: Rotavirus |
Molecular weight | Theoretical: 126.326 KDa |
-Macromolecule #2: dsRNA
Macromolecule | Name: dsRNA / type: rna / ID: 2 / Name.synonym: dsRNA / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: Bovine rotavirus / synonym: Rotavirus |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.4 |
Grid | Details: Lacy carbon and C-flat |
Vitrification | Cryogen 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 |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Average: 90 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected |
Date | Jun 1, 2007 |
Image recording | Category: 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated 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 stage | Specimen holder: Eucentric, side-entry / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Phase-flipping |
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Final reconstruction | Applied 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 |