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Yorodumi- PDB-6hwi: Immature M-PMV capsid hexamer structure in intact virus particles -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hwi | ||||||||||||||||||||||||||||||
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Title | Immature M-PMV capsid hexamer structure in intact virus particles | ||||||||||||||||||||||||||||||
Components | Gag-Pro-Pol polyprotein | ||||||||||||||||||||||||||||||
Keywords | VIRAL PROTEIN / M-PMV / capsid / hexamer | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / viral process / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / viral process / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Mason-Pfizer monkey virus | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.2 Å | ||||||||||||||||||||||||||||||
Authors | Qu, K. / Glass, B. / Dolezal, M. / Schur, F.K.M. / Rein, A. / Rumlova, M. / Ruml, T. / Kraeusslich, H.G. / Briggs, J.A.G. | ||||||||||||||||||||||||||||||
Funding support | Germany, United Kingdom, Czech Republic, 9items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Structure and architecture of immature and mature murine leukemia virus capsids. Authors: Kun Qu / Bärbel Glass / Michal Doležal / Florian K M Schur / Brice Murciano / Alan Rein / Michaela Rumlová / Tomáš Ruml / Hans-Georg Kräusslich / John A G Briggs / Abstract: Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as ...Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein-protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6hwi.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hwi.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 6hwi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hwi_validation.pdf.gz | 850.9 KB | Display | wwPDB validaton report |
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Full document | 6hwi_full_validation.pdf.gz | 853.8 KB | Display | |
Data in XML | 6hwi_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 6hwi_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/6hwi ftp://data.pdbj.org/pub/pdb/validation_reports/hw/6hwi | HTTPS FTP |
-Related structure data
Related structure data | 0290MC 0291C 0292C 0293C 4419C 4421C 4422C 6gzaC 6hwwC 6hwxC 6hwyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 21817.359 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mason-Pfizer monkey virus / Gene: gag-pro-pol / Production host: Homo sapiens (human) / References: UniProt: P07572, UniProt: P07570*PLUS |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Mason-Pfizer monkey virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Mason-Pfizer monkey virus |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK 293T / Plasmid: pSHRM15 D26N |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Purified virus solution was inactivated and diluted 1:1 with PBS containing 10 nm colloidal gold. |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1 |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 288 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.6 sec. / Electron dose: 2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 Details: Dose fluctuation was caused by the ring collapse of FEG during data collection. |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 6 / Used frames/image: 1-6 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17109 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 34 / Num. of volumes extracted: 17109 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |