[English] 日本語
Yorodumi
- EMDB-13086: Representative cryo-electron tomogram of mature HIV-1 particles -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13086
TitleRepresentative cryo-electron tomogram of mature HIV-1 particles
Map dataRepresentative cryo-electron tomogram of mature HIV-1 particles
Sample
  • Virus: Human immunodeficiency virus 1
Biological speciesHuman immunodeficiency virus 1
Methodelectron tomography / cryo EM
AuthorsQu K / Ke ZL / Zila V / Anders-Oesswein M / Glass B / Muecksch F / Mueller R / Schultz C / Mueller B / Kraeusslich HG / Briggs JAG
Funding supportEuropean Union, United Kingdom, Germany, United States, 8 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-648432 MEMBRANEFUSIONEuropean Union
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
German Research Foundation (DFG)112927078 - TRR 83 Germany
German Research Foundation (DFG)240245660 - SFB1129 project 5 Germany
German Research Foundation (DFG)MU885-1 Germany
German Research Foundation (DFG)240245660 - SFB1129 project 6 Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127631 United States
German Research Foundation (DFG)278001972 - TRR186 project Z1 Germany
CitationJournal: Science / Year: 2021
Title: Maturation of the matrix and viral membrane of HIV-1.
Authors: Kun Qu / Zunlong Ke / Vojtech Zila / Maria Anders-Össwein / Bärbel Glass / Frauke Mücksch / Rainer Müller / Carsten Schultz / Barbara Müller / Hans-Georg Kräusslich / John A G Briggs /
Abstract: Gag, the primary structural protein of HIV-1, is recruited to the plasma membrane for virus assembly by its matrix (MA) domain. Gag is subsequently cleaved into its component domains, causing ...Gag, the primary structural protein of HIV-1, is recruited to the plasma membrane for virus assembly by its matrix (MA) domain. Gag is subsequently cleaved into its component domains, causing structural maturation to repurpose the virion for cell entry. We determined the structure and arrangement of MA within immature and mature HIV-1 through cryo-electron tomography. We found that MA rearranges between two different hexameric lattices upon maturation. In mature HIV-1, a lipid extends out of the membrane to bind with a pocket in MA. Our data suggest that proteolytic maturation of HIV-1 not only assembles the viral capsid surrounding the genome but also repurposes the membrane-bound MA lattice for an entry or postentry function and results in the partial removal of up to 2500 lipids from the viral membrane.
History
DepositionJun 15, 2021-
Header (metadata) releaseAug 18, 2021-
Map releaseAug 18, 2021-
UpdateAug 25, 2021-
Current statusAug 25, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Supplemental images

emd_13086.png

Downloads & links

-
Map

FileDownload / File: emd_13086.map.gz / Format: CCP4 / Size: 78.6 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationRepresentative cryo-electron tomogram of mature HIV-1 particles
Voxel sizeX=Y=Z: 11.088 Å
Density
Minimum - Maximum-1399.0 - 789.0
Average (Standard dev.)23.395866 (±113.23807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720511112
Spacing511720112
CellA: 5665.9683 Å / B: 7983.3604 Å / C: 1241.8561 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z11.08811.08811.088
M x/y/z511720112
origin x/y/z0.0000.0000.000
length x/y/z5665.9687983.3601241.856
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ332332332
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS511720112
D min/max/mean-1399.000789.00023.396

-
Supplemental data

-
Sample components

-
Entire : Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Components
  • Virus: Human immunodeficiency virus 1

-
Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0
Details: Mature cHIV virus particles purified from HEK293T cells.
NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host systemOrganism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE
DetailsMature cHIV virus particles purified from HEK293T cells.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: homemade / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionNumber images used: 1
CTF correctionSoftware: (Name: CTFFIND, IMOD)

+
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://pdbjlvh1.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