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Yorodumi- EMDB-2090: Structure of the immature retroviral capsid at 8A resolution by c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2090 | |||||||||
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Title | Structure of the immature retroviral capsid at 8A resolution by cryo-electron microscopy | |||||||||
Map data | Reconstruction of the M-PMV CANC Gag dimer | |||||||||
Sample |
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Keywords | retrovirus / capsid / gag | |||||||||
Function / homology | Function and homology information virion component => GO:0044423 / viral budding via host ESCRT complex / viral process / viral nucleocapsid / host cell cytoplasm / nucleic acid binding / structural constituent of virion / viral translational frameshifting / zinc ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Mason-Pfizer monkey virus | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 7.0 Å | |||||||||
Authors | Bharat TAM / Davey NE / Ulbrich P / Riches JD / de Marco A / Rumlova M / Sachse C / Ruml T / Briggs JAG | |||||||||
Citation | Journal: Nature / Year: 2012 Title: Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy. Authors: Tanmay A M Bharat / Norman E Davey / Pavel Ulbrich / James D Riches / Alex de Marco / Michaela Rumlova / Carsten Sachse / Tomas Ruml / John A G Briggs / Abstract: The assembly of retroviruses such as HIV-1 is driven by oligomerization of their major structural protein, Gag. Gag is a multidomain polyprotein including three conserved folded domains: MA (matrix), ...The assembly of retroviruses such as HIV-1 is driven by oligomerization of their major structural protein, Gag. Gag is a multidomain polyprotein including three conserved folded domains: MA (matrix), CA (capsid) and NC (nucleocapsid). Assembly of an infectious virion proceeds in two stages. In the first stage, Gag oligomerization into a hexameric protein lattice leads to the formation of an incomplete, roughly spherical protein shell that buds through the plasma membrane of the infected cell to release an enveloped immature virus particle. In the second stage, cleavage of Gag by the viral protease leads to rearrangement of the particle interior, converting the non-infectious immature virus particle into a mature infectious virion. The immature Gag shell acts as the pivotal intermediate in assembly and is a potential target for anti-retroviral drugs both in inhibiting virus assembly and in disrupting virus maturation. However, detailed structural information on the immature Gag shell has not previously been available. For this reason it is unclear what protein conformations and interfaces mediate the interactions between domains and therefore the assembly of retrovirus particles, and what structural transitions are associated with retrovirus maturation. Here we solve the structure of the immature retroviral Gag shell from Mason-Pfizer monkey virus by combining cryo-electron microscopy and tomography. The 8-Å resolution structure permits the derivation of a pseudo-atomic model of CA in the immature retrovirus, which defines the protein interfaces mediating retrovirus assembly. We show that transition of an immature retrovirus into its mature infectious form involves marked rotations and translations of CA domains, that the roles of the amino-terminal and carboxy-terminal domains of CA in assembling the immature and mature hexameric lattices are exchanged, and that the CA interactions that stabilize the immature and mature viruses are almost completely distinct. | |||||||||
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_2090.map.gz | 773.4 KB | EMDB map data format | |
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Header (meta data) | emd-2090-v30.xml emd-2090.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | emd_2090.jpg | 180.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2090 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2090 | HTTPS FTP |
-Validation report
Data in XML | emd_2090_validation.xml.gz | 5 KB | Display | |
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Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2090 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2090 | HTTPS FTP |
-Related structure data
Related structure data | 4ardMC 4argMC 2089C M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_2090.map.gz / Format: CCP4 / Size: 825.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the M-PMV CANC Gag dimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.53 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 : M-PMV CANC Gag dimer
Entire | Name: M-PMV CANC Gag dimer |
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Components |
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-Supramolecule #1000: M-PMV CANC Gag dimer
Supramolecule | Name: M-PMV CANC Gag dimer / type: sample / ID: 1000 / Oligomeric state: Helical / Number unique components: 1 |
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-Macromolecule #1: M-PMV dPro CANC protein
Macromolecule | Name: M-PMV dPro CANC protein / type: protein_or_peptide / ID: 1 / Oligomeric state: Helical / Recombinant expression: Yes |
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Source (natural) | Organism: Mason-Pfizer monkey virus |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.7 / Details: 50mM Tris, 100mM NaCl, 1uM Zn |
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Grid | Details: 300 mesh copper, glow discharged |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Apr 23, 2012 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 46 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -4.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder: Liquid nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Reconstruction carried out using real-space helical reconstruction followed by 3D averaging of the asymmetric unit from assemblies with different helical symmetry parameters. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: OTHER / Software - Name: Spider, AV3 |
CTF correction | Details: Division by 3D CTF^2 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: UCSF Chimera |
Details | Protocol: Rigid body. Two copies of the M-PMV CA-NTD domain were fitted separately. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4ard: PDB-4arg: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: UCSF Chimera |
Details | Protocol: Rigid body. Two copies of the CA-NTD domain were fitted separately. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4ard: PDB-4arg: |
-Atomic model buiding 3
Initial model | PDB ID: Chain - Chain ID: L |
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Software | Name: UCSF Chimera |
Details | Protocol: Rigid body. Two copies of the CA-CTD domains were fitted separately. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4ard: PDB-4arg: |