|Entry||Database: PDB / ID: 6hwi|
|Title||Immature M-PMV capsid hexamer structure in intact virus particles|
|Keywords||VIRAL PROTEIN / M-PMV / capsid / hexamer|
|Function / homology||Reverse transcriptase thumb / dUTPase-like / Ribonuclease H domain / Integrase, N-terminal zinc-binding domain / Beta-retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / Retroviral matrix protein / Ribonuclease H-like superfamily / Integrase-like, N-terminal ...Reverse transcriptase thumb / dUTPase-like / Ribonuclease H domain / Integrase, N-terminal zinc-binding domain / Beta-retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / Retroviral matrix protein / Ribonuclease H-like superfamily / Integrase-like, N-terminal / Retropepsins / Aspartic peptidase domain superfamily / dUTPase, trimeric / Aspartic peptidase, active site / Retropepsin-like catalytic domain / dUTPase-like superfamily / Ribonuclease H superfamily / Integrase, C-terminal domain superfamily, retroviral / Zinc finger, CCHC-type superfamily / Beta-retroviral matrix superfamily / RNase H / Retroviral aspartyl protease / Reverse transcriptase (RNA-dependent DNA polymerase) / Integrase DNA binding domain / gag gene protein p24 (core nucleocapsid protein) / Peptidase A2A, retrovirus, catalytic / Zinc finger, CCHC-type / dUTPase / Reverse transcriptase thumb domain / Integrase DNA binding domain profile. / Integrase catalytic domain profile. / RNase H domain profile. / Reverse transcriptase (RT) catalytic domain profile. / Zinc finger integrase-type profile. / Aspartyl protease, retroviral-type family profile. / G-patch domain profile. / Zinc finger CCHC-type profile. / Integrase, catalytic core / Eukaryotic and viral aspartyl proteases active site. / Integrase Zinc binding domain / Retroviral GAG p10 protein / G-patch domain / G-patch domain / Reverse transcriptase domain / Retroviral nucleocapsid protein Gag / Integrase, C-terminal, retroviral / Integrase core domain / dUTP diphosphatase / dUTP diphosphatase activity / structural constituent of virion / Hydrolases, Acting on peptide bonds (peptidases), Aspartic endopeptidases / ribonuclease H / RNA-directed DNA polymerase / DNA integration / viral genome integration into host DNA / Transferases, Transferring phosphorus-containing groups, Nucleotidyltransferases / RNA-directed DNA polymerase activity / establishment of integrated proviral latency / RNA-DNA hybrid ribonuclease activity / viral entry into host cell / viral nucleocapsid / DNA recombination / Hydrolases, Acting on ester bonds / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / RNA binding / DNA binding / zinc ion binding / Gag-Pro-Pol polyprotein|
Function and homology information
|Specimen source||Mason-Pfizer monkey virus|
|Method||ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / 7.2 Å resolution|
|Authors||Qu, K. / Glass, B. / Dolezal, M. / Schur, F.K.M. / Rein, A. / Rumlova, M. / Ruml, T. / Kraeusslich, H.G. / Briggs, J.A.G.|
|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.
SummaryFull reportAbout validation report
|Date||Deposition: Oct 12, 2018 / Release: Dec 5, 2018|
|Structure viewer||Molecule: |
Downloads & links
A: Gag-Pro-Pol polyprotein
B: Gag-Pro-Pol polyprotein
C: Gag-Pro-Pol polyprotein
A: Gag-Pro-Pol polyproteinx 6
B: Gag-Pro-Pol polyprotein
C: Gag-Pro-Pol polyprotein
Mass: 21817.359 Da / Num. of mol.: 3 / Source: (gene. exp.) Mason-Pfizer monkey virus / Gene: gag-pro-pol / Production host: Homo sapiens (human) / References: UniProt: P07572
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: subtomogram averaging|
|Component||Name: Mason-Pfizer monkey virus / Type: VIRUS / Entity ID: 1 / Source: RECOMBINANT|
|Source (natural)||Organism: Mason-Pfizer monkey virus|
|Source (recombinant)||Cell: HEK 293T / Organism: Homo sapiens (human) / Plasmid: pSHRM15 D26N|
|Details of virus||Empty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION|
|Buffer solution||pH: 6|
|Specimen||Details: Purified virus solution was inactivated and diluted 1:1 with PBS containing 10 nm colloidal gold.|
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
|Specimen support||Grid material: COPPER / Grid mesh size: 300 / Grid type: C-flat-2/1|
|Vitrification||Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 288|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 / Nominal defocus max: 4500 / Nominal defocus min: 2000 / Cs: 2.7 / C2 aperture diameter: 50 / Alignment procedure: ZEMLIN TABLEAU|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 0.6 / Electron dose: 2|
Details: Dose fluctuation was caused by the ring collapse of FEG during data collection.
Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 1
|EM imaging optics||Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20|
|Image scans||Sampling size: 5 / Width: 3710 / Height: 3838 / Movie frames/image: 6 / Used frames/image: 1-6|
|CTF correction||Type: PHASE FLIPPING ONLY|
|Symmetry||Point symmetry: C6|
|3D reconstruction||Resolution: 7.2 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 17109 / Symmetry type: POINT|
|EM volume selection||Number of tomograms: 34 / Number of volumes extracted: 17109|
|Atomic model building||Ref protocol: FLEXIBLE FIT / Ref space: REAL|
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi