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Yorodumi- EMDB-1238: Infectious bursal disease virus capsid assembly and maturation by... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1238 | |||||||||
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Title | Infectious bursal disease virus capsid assembly and maturation by structural rearrangements of a transient molecular switch. | |||||||||
Map data | Density map of the Infectious Bursal Disease Virus (IBDV) capsid 2X2Y2Z oriented. | |||||||||
Sample |
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Biological species | Infectious bursal disease virus (Gumboro virus) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 10.4 Å | |||||||||
Authors | Luque D / Saugar I / Rodriguez JF / Verdaguer N / Garriga D / San Martin C / Velazquez-Muriel JA / Trus BL / Carrascosa JL / Caston JR | |||||||||
Citation | Journal: J Virol / Year: 2007 Title: Infectious bursal disease virus capsid assembly and maturation by structural rearrangements of a transient molecular switch. Authors: Daniel Luque / Irene Saugar / José F Rodríguez / Nuria Verdaguer / Damiá Garriga / Carmen San Martín / Javier A Velázquez-Muriel / Benes L Trus / José L Carrascosa / José R Castón / Abstract: Infectious bursal disease virus (IBDV), a double-stranded RNA (dsRNA) virus belonging to the Birnaviridae family, is an economically important avian pathogen. The IBDV capsid is based on a single- ...Infectious bursal disease virus (IBDV), a double-stranded RNA (dsRNA) virus belonging to the Birnaviridae family, is an economically important avian pathogen. The IBDV capsid is based on a single-shelled T=13 lattice, and the only structural subunits are VP2 trimers. During capsid assembly, VP2 is synthesized as a protein precursor, called pVP2, whose 71-residue C-terminal end is proteolytically processed. The conformational flexibility of pVP2 is due to an amphipathic alpha-helix located at its C-terminal end. VP3, the other IBDV major structural protein that accomplishes numerous roles during the viral cycle, acts as a scaffolding protein required for assembly control. Here we address the molecular mechanism that defines the multimeric state of the capsid protein as hexamers or pentamers. We used a combination of three-dimensional cryo-electron microscopy maps at or close to subnanometer resolution with atomic models. Our studies suggest that the key polypeptide element, the C-terminal amphipathic alpha-helix, which acts as a transient conformational switch, is bound to the flexible VP2 C-terminal end. In addition, capsid protein oligomerization is also controlled by the progressive trimming of its C-terminal domain. The coordination of these molecular events correlates viral capsid assembly with different conformations of the amphipathic alpha-helix in the precursor capsid, as a five-alpha-helix bundle at the pentamers or an open star-like conformation at the hexamers. These results, reminiscent of the assembly pathway of positive single-stranded RNA viruses, such as nodavirus and tetravirus, add new insights into the evolutionary relationships of dsRNA viruses. | |||||||||
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_1238.map.gz | 81.7 MB | EMDB map data format | |
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Header (meta data) | emd-1238-v30.xml emd-1238.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | 1238.gif | 14.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1238 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1238 | HTTPS FTP |
-Validation report
Summary document | emd_1238_validation.pdf.gz | 317.7 KB | Display | EMDB validaton report |
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Full document | emd_1238_full_validation.pdf.gz | 316.7 KB | Display | |
Data in XML | emd_1238_validation.xml.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1238 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1238 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1238.map.gz / Format: CCP4 / Size: 86.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Density map of the Infectious Bursal Disease Virus (IBDV) capsid 2X2Y2Z oriented. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 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 : Infectious Bursal Disease Virus
Entire | Name: Infectious Bursal Disease Virus (Gumboro virus) |
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Components |
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-Supramolecule #1000: Infectious Bursal Disease Virus
Supramolecule | Name: Infectious Bursal Disease Virus / type: sample / ID: 1000 / Oligomeric state: 780 copies of VP2 arranged in 260 trimers / Number unique components: 1 |
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Molecular weight | Theoretical: 38 MDa |
-Supramolecule #1: Infectious bursal disease virus
Supramolecule | Name: Infectious bursal disease virus / type: virus / ID: 1 / Name.synonym: IBDV / NCBI-ID: 10995 / Sci species name: Infectious bursal disease virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: IBDV |
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Host (natural) | Organism: Gallus gallus (chicken) / synonym: VERTEBRATES |
Molecular weight | Experimental: 38 MDa |
Virus shell | Shell ID: 1 / Name: IBDV / Diameter: 700 Å / T number (triangulation number): 13 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.2 / Details: 25 mM PIPES, 150 mM NaCl, and 20 mM CaCl2 |
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Staining | Type: NEGATIVE Details: Samples containing were applied to one side of a holey carbon film, washed twice on water drops, blotted, and plunged into a liquid ethane bath following standard procedures |
Grid | Details: 300 mesh holey carbon film |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Image recording | Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 129 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.4 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: em3dr2 / Number images used: 9483 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: SITUS and URO |
Details | Protocol: Rigid body. Refinement was done in both Real and Fourier Space |
Refinement | Protocol: RIGID BODY FIT / Target criteria: CC and R-factor |