+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1609 | |||||||||
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Title | VP6-VP7 complex structure from VP7 recoated rotavirus DLP | |||||||||
Map data | T13 non-icosahedral local averaging | |||||||||
Sample |
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Keywords | rotavirus / capsid / VP7 / VP6 / VP2 | |||||||||
Function / homology | Function and homology information viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral inner capsid / viral outer capsid / viral nucleocapsid / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral inner capsid / viral outer capsid / viral nucleocapsid / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Chen JZ / Settembre EC / Aoki ST / Zhang X / Bellamy AR / Dormitzer PR / Harrison SC / Grigorieff N | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2009 Title: Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM. Authors: James Z Chen / Ethan C Settembre / Scott T Aoki / Xing Zhang / A Richard Bellamy / Philip R Dormitzer / Stephen C Harrison / Nikolaus Grigorieff / Abstract: Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle ...Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle reconstruction, we have visualized a rotavirus particle comprising the inner capsid coated with the trimeric outer-layer protein, VP7, at a resolution (4 A) comparable with that of X-ray crystallography. We have traced the VP7 polypeptide chain, including parts not seen in its X-ray crystal structure. The 3 well-ordered, 30-residue, N-terminal "arms" of each VP7 trimer grip the underlying trimer of VP6, an inner-capsid protein. Structural differences between free and particle-bound VP7 and between free and VP7-coated inner capsids may regulate mRNA transcription and release. The Ca(2+)-stabilized VP7 intratrimer contact region, which presents important neutralizing epitopes, is unaltered upon capsid binding. | |||||||||
History |
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-Structure visualization
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1609.map.gz | 3 MB | EMDB map data format | |
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Header (meta data) | emd-1609-v30.xml emd-1609.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | T13_ave_icon.tif | 732.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1609 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1609 | HTTPS FTP |
-Validation report
Summary document | emd_1609_validation.pdf.gz | 297.1 KB | Display | EMDB validaton report |
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Full document | emd_1609_full_validation.pdf.gz | 296.3 KB | Display | |
Data in XML | emd_1609_validation.xml.gz | 4.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1609 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1609 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1609.map.gz / Format: CCP4 / Size: 3.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | T13 non-icosahedral local averaging | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.233 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : VP7 recoated rotavirus DLP
Entire | Name: VP7 recoated rotavirus DLP |
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Components |
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-Supramolecule #1000: VP7 recoated rotavirus DLP
Supramolecule | Name: VP7 recoated rotavirus DLP / type: sample / ID: 1000 / Oligomeric state: icosahedral virus capsid / Number unique components: 3 |
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Molecular weight | Experimental: 60 MDa / Theoretical: 60 MDa / Method: Sum of all components |
-Macromolecule #1: VP7
Macromolecule | Name: VP7 / type: protein_or_peptide / ID: 1 / Name.synonym: VP7 / Number of copies: 780 / Oligomeric state: Trimer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: Bovine |
Molecular weight | Experimental: 37.4 KDa / Theoretical: 37.4 KDa |
-Macromolecule #2: VP6
Macromolecule | Name: VP6 / type: protein_or_peptide / ID: 2 / Name.synonym: VP6 / Number of copies: 780 / Oligomeric state: Trimer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: Bovine |
Molecular weight | Experimental: 44.8 KDa / Theoretical: 44.8 KDa |
-Macromolecule #3: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 3 / Name.synonym: VP2 / Number of copies: 120 / Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: Bovine |
Molecular weight | Experimental: 94 KDa / Theoretical: 94 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.0 mg/mL |
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Buffer | pH: 8 / Details: 20mM Tris-HCl, 50mM NaCl, 2mM CaCl2 |
Grid | Details: C-flat grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger / Method: Blot for 3 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Min: 90 K / Max: 90 K / Average: 90 K |
Date | Dec 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: 148 / Average electron dose: 25 e/Å2 / Od range: 1.2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 58168 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected using SIGNATURE, the density map was reconstructed and refined using FREALIGN. |
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CTF correction | Details: Individual particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 3780 |