[English] 日本語
Yorodumi- EMDB-0290: Immature M-PMV capsid hexamer structure in intact virus particles -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0290 | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Immature M-PMV capsid hexamer structure in intact virus particles | ||||||||||||||||||||||||||||||
Map data | None | ||||||||||||||||||||||||||||||
Sample |
| ||||||||||||||||||||||||||||||
Keywords | M-PMV / capsid / hexamer / VIRAL PROTEIN | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 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 / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Mason-Pfizer monkey virus | ||||||||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 7.2 Å | ||||||||||||||||||||||||||||||
Authors | Qu K / Glass B | ||||||||||||||||||||||||||||||
Funding support | Germany, United Kingdom, Czech Republic, 9 items
| ||||||||||||||||||||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0290.map.gz | 24.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-0290-v30.xml emd-0290.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_0290.png | 385.1 KB | ||
Filedesc metadata | emd-0290.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0290 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0290 | HTTPS FTP |
-Validation report
Summary document | emd_0290_validation.pdf.gz | 521.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_0290_full_validation.pdf.gz | 521.3 KB | Display | |
Data in XML | emd_0290_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | emd_0290_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0290 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0290 | HTTPS FTP |
-Related structure data
Related structure data | 6hwiMC 0291C 0292C 0293C 4419C 4421C 4422C 6gzaC 6hwwC 6hwxC 6hwyC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_0290.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Mason-Pfizer monkey virus
Entire | Name: Mason-Pfizer monkey virus |
---|---|
Components |
|
-Supramolecule #1: Mason-Pfizer monkey virus
Supramolecule | Name: Mason-Pfizer monkey virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11855 / Sci species name: Mason-Pfizer monkey virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
---|
-Macromolecule #1: Gag-Pro-Pol polyprotein
Macromolecule | Name: Gag-Pro-Pol polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mason-Pfizer monkey virus |
Molecular weight | Theoretical: 21.817359 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GFDFAVIKEL KTAASQYGAT APYTLAIVES VADNWLTPTD WNTLVRAVLS GGDHLLWKSE FFENCRDTAK RNQQAGNGWD FDMLTGSGN YSSTDAQMQY DPGLFAQIQA AATKAWRKLP VKGDPGASLT GVKQGPDEPF ADFVHRLITT AGRIFGSAEA G VDYVKQLA ...String: GFDFAVIKEL KTAASQYGAT APYTLAIVES VADNWLTPTD WNTLVRAVLS GGDHLLWKSE FFENCRDTAK RNQQAGNGWD FDMLTGSGN YSSTDAQMQY DPGLFAQIQA AATKAWRKLP VKGDPGASLT GVKQGPDEPF ADFVHRLITT AGRIFGSAEA G VDYVKQLA YENANPACQA AIRPYRKKTD LTGYIRLCSD IG UniProtKB: Gag-Pro-Pol polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6 |
---|---|
Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK II |
Details | Purified virus solution was inactivated and diluted 1:1 with PBS containing 10 nm colloidal gold. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-6 / Number grids imaged: 1 / Average exposure time: 0.6 sec. / Average electron dose: 2.0 e/Å2 Details: Dose fluctuation was caused by the ring collapse of FEG during data collection. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: AV3, TOM) / Number subtomograms used: 17109 | ||||||
---|---|---|---|---|---|---|---|
Extraction | Number tomograms: 34 / Number images used: 17109 Software:
| ||||||
Final angle assignment | Type: OTHER / Software: (Name: AV3, TOM) / Details: Subtomogram Averaging. |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
---|---|
Output model | PDB-6hwi: |