[English] 日本語
Yorodumi
- PDB-6hwi: Immature M-PMV capsid hexamer structure in intact virus particles -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6hwi
TitleImmature M-PMV capsid hexamer structure in intact virus particles
ComponentsGag-Pro-Pol polyprotein
KeywordsVIRAL PROTEIN / M-PMV / capsid / hexamer
Function / homologyReverse 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 / Aspartic endopeptidases / calf thymus ribonuclease H / RNA-directed DNA polymerase / DNA integration / viral genome integration into host DNA / 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 / 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 sourceMason-Pfizer monkey virus
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / 7.2 Å resolution
AuthorsQu, K. / Glass, B. / Dolezal, M. / Schur, F.K.M. / Rein, A. / Rumlova, M. / Ruml, T. / Kraeusslich, H.G. / Briggs, J.A.G.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 12, 2018 / Release: Dec 5, 2018

-
Structure visualization

Movie
  • Biological unit as author_defined_assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-0290
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0290
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gag-Pro-Pol polyprotein
B: Gag-Pro-Pol polyprotein
C: Gag-Pro-Pol polyprotein


Theoretical massNumber of molelcules
Total (without water)65,4523
Polyers65,4523
Non-polymers00
Water0
1
A: Gag-Pro-Pol polyprotein
B: Gag-Pro-Pol polyprotein
C: Gag-Pro-Pol polyprotein
x 6


Theoretical massNumber of molelcules
Total (without water)392,71218
Polyers392,71218
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
build point asymmetric unit5

-
Components

#1: Protein/peptide Gag-Pro-Pol polyprotein / Pr180


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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: Mason-Pfizer monkey virusSimian retrovirus / 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 virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Buffer solutionpH: 6
SpecimenDetails: 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 supportGrid material: COPPER / Grid mesh size: 300 / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 288 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 microns / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.6 sec. / Electron dose: 2 e/Å2
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 opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansSampling size: 5 microns / Width: 3710 / Height: 3838 / Movie frames/image: 6 / Used frames/image: 1-6

-
Processing

EM software
IDNameCategoryDetails
1AmiraFPMvolume selectionVolume selection
2MATLABvolume selectionVolume extraction
3SerialEMimage acquisitionDose-symmetric tilt-scheme
5MATLABCTF correctionCTF determination
6IMODCTF correctionPhase flipping only
9Cootmodel fitting
10UCSF Chimeramodel fitting
12PHENIXmodel refinement
14AV3final Euler assignment
15TOMfinal Euler assignment
17AV33D reconstruction
18TOM3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C6
3D reconstructionResolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 17109 / Symmetry type: POINT
EM volume selectionNumber of tomograms: 34 / Number of volumes extracted: 17109
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL

+
About Yorodumi

-
News

-
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.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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

Read more