[English] 日本語
Yorodumi
- PDB-6hwy: Mature MLV capsid pentamer structure in intact virus particles -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hwy
TitleMature MLV capsid pentamer structure in intact virus particles
ComponentsPutative gag polyproteinGroup-specific antigen
KeywordsVIRAL PROTEIN / MLV / capsid / pentamer
Function / homology
Function and homology information


virion assembly / viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / structural constituent of virion / nucleic acid binding / host cell plasma membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger ...Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Putative gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesMurine leukemia virus
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8.6 Å
AuthorsQu, 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
OrganizationGrant numberCountry
German Research FoundationBR 3635/2-1 Germany
German Research FoundationKR 906/7-1 Germany
German Research FoundationKR 906/8-1 Germany
European Research CouncilERC-CoG-648432 Germany
Medical Research Council (United Kingdom)MC_UP_1201/16 United Kingdom
Czech Science Foundation17-25602S Czech Republic
Ministry of Education (Czech Republic)LO1302 Czech Republic
Ministry of Education (Czech Republic)LO1304 Czech Republic
Ministry of Education (Czech Republic)LO1601 Czech Republic
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.
History
DepositionOct 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: em_admin / entity_src_gen / pdbx_database_proc
Item: _em_admin.last_update / _entity_src_gen.pdbx_host_org_cell_line

-
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-0293
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0293
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative gag polyprotein
B: Putative gag polyprotein
C: Putative gag polyprotein
D: Putative gag polyprotein


Theoretical massNumber of molelcules
Total (without water)108,6614
Polymers108,6614
Non-polymers00
Water0
1
A: Putative gag polyprotein
B: Putative gag polyprotein
C: Putative gag polyprotein
D: Putative gag polyprotein
x 5


Theoretical massNumber of molelcules
Total (without water)543,30620
Polymers543,30620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation4

-
Components

#1: Protein
Putative gag polyprotein / Group-specific antigen


Mass: 27165.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine leukemia virus / Gene: gag / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: A0A240FAQ8, UniProt: P03336*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: Murine leukemia virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Murine leukemia virus
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK 293T / Plasmid: M2204
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 6
SpecimenEmbedding 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 supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: 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
MicroscopyModel: 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 X / Nominal defocus max: 7500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.6 sec. / Electron dose: 1.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 2
Details: Dose fluctuation was caused by the ring collapse of FEG during data collection.
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansSampling size: 5 µm / 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
13AV3final Euler assignment
14TOMfinal Euler assignment
16AV33D reconstruction
17TOM3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1299 / Algorithm: BACK PROJECTION / Symmetry type: POINT
EM volume selectionNum. of tomograms: 65 / Num. of volumes extracted: 1299
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-IDPdb chain residue range
11U7KA11-131
26GZAA11-87

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
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.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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