[English] 日本語
Yorodumi
- EMDB-2707: The structure of the immature M-PMV capsid in intact virus particles -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2707
TitleThe structure of the immature M-PMV capsid in intact virus particles
Map dataSubtomogram averaging reconstruction of the immature Mason-Pfizer monkey virus capsid from intact virus particles
Sample
  • Sample: intact Mason-Pfizer Monkey virus particles
  • Virus: Mason-Pfizer monkey virus
Keywordsimmature M-PMV / Mason-Pfizer Monkey virus / Retrovirus / Maturation / capsid / Gag
Biological speciesMason-Pfizer monkey virus
Methodsubtomogram averaging / cryo EM / Resolution: 9.7 Å
AuthorsSchur FKM / Hagen WJH / Rumlova M / Ruml T / Mueller B / Kraeusslich H-G / Briggs JAG
CitationJournal: Nature / Year: 2015
Title: Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution.
Authors: Florian K M Schur / Wim J H Hagen / Michaela Rumlová / Tomáš Ruml / Barbara Müller / Hans-Georg Kräusslich / John A G Briggs /
Abstract: Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the ...Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the infected cell, inducing budding and release of an immature particle. Second, Gag is cleaved by the viral protease, leading to internal rearrangement of the virus into the mature, infectious form. Immature and mature HIV-1 particles are heterogeneous in size and morphology, preventing high-resolution analysis of their protein arrangement in situ by conventional structural biology methods. Here we apply cryo-electron tomography and sub-tomogram averaging methods to resolve the structure of the capsid lattice within intact immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning of all α-helices. The resulting model reveals tertiary and quaternary structural interactions that mediate HIV-1 assembly. Strikingly, these interactions differ from those predicted by the current model based on in vitro-assembled arrays of Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference, we solve the structure of the capsid lattice within intact immature Mason-Pfizer monkey virus particles. Comparison with the immature HIV-1 structure reveals that retroviral capsid proteins, while having conserved tertiary structures, adopt different quaternary arrangements during virus assembly. The approach demonstrated here should be applicable to determine structures of other proteins at subnanometre resolution within heterogeneous environments.
History
DepositionJul 10, 2014-
Header (metadata) releaseAug 6, 2014-
Map releaseNov 5, 2014-
UpdateJan 21, 2015-
Current statusJan 21, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.114
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.114
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2707.tif

Downloads & links

-
Map

FileDownload / File: emd_2707.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram averaging reconstruction of the immature Mason-Pfizer monkey virus capsid from intact virus particles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.03 Å/pix.
x 140 pix.
= 283.5 Å		2.03 Å/pix.
x 140 pix.
= 283.5 Å		2.03 Å/pix.
x 140 pix.
= 283.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.025 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.114 / Movie #1: 0.114
Minimum - Maximum-0.35433057 - 0.46596488
Average (Standard dev.)-0.00307267 (±0.04790109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 283.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.0252.0252.025
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z283.500283.500283.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-180-180-179
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.3540.466-0.003

-
Supplemental data

-
Sample components

-
Entire : intact Mason-Pfizer Monkey virus particles

EntireName: intact Mason-Pfizer Monkey virus particles
Components
  • Sample: intact Mason-Pfizer Monkey virus particles
  • Virus: Mason-Pfizer monkey virus

-
Supramolecule #1000: intact Mason-Pfizer Monkey virus particles

SupramoleculeName: intact Mason-Pfizer Monkey virus particles / type: sample / ID: 1000
Details: The virus contained an inactivating mutation in the protease (D26N)
Oligomeric state: Homohexameric / Number unique components: 1

-
Supramolecule #1: Mason-Pfizer monkey virus

SupramoleculeName: Mason-Pfizer monkey virus / type: virus / ID: 1 / Name.synonym: M-PMV / NCBI-ID: 11855 / Sci species name: Mason-Pfizer monkey virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: M-PMV
Host (natural)Organism: Cercopithecidae (Old World monkeys) / synonym: VERTEBRATES
Host systemRecombinant cell: HEK293T / Recombinant plasmid: pSARM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferDetails: PBS
GridDetails: C-Flat 2/2-3C glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II
Method: Degassed C-Flat 2/2-3C grids were glow discharged for 30 seconds at 20 mA. Virus solution was diluted in PBS containing 10nm colloidal gold. 2 ul of this mixture was applied to a grid. Blotting time: 2 seconds

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at nominal working magnification
Specialist opticsEnergy filter - Name: GATAN GIF 2002
DateFeb 3, 2014
Image recordingCategory: CCD / Film or detector model: GATAN MULTISCAN / Average electron dose: 40 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 42000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -45 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

DetailsSubtomogram averaging calculations were performed using the AV3 and TOM packages. Subtomograms were extracted from the surface of the virus.
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: OTHER / Software - Name: TOM, AV3
Details: Reconstruction carried out using subtomogram averaging. Subtomogram averaging was performed using scripts from the TOM (Nickell et al, 2005) and AV3 (Foerster et al, 2005) packages.
Number subtomograms used: 12920
CTF correctionDetails: Phase flipping of individual tilts

+
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