[English] 日本語
Yorodumi
- EMDB-5321: Molecular structure of soluble trimeric HIV-1 glycoprotein gp140 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5321
TitleMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with sCD4
Map dataMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with sCD4
Sample
  • Sample: SOSIP gp140 KNH1144 sCD4
  • Protein or peptide: SOSIP gp140 KNH1144 sCD4
KeywordsHIV/AIDS vaccine / immunogen / HIV glycoprotein structure / gp140 trimer / cryo-electron tomography / sub-tomogram averaging / cryo-electron microscopy
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsHarris A / Borgnia MJ / Shi D / Bartesaghi A / He H / Pejchal R / Kang YK / Depetris R / Marozsan AJ / Sanders RW ...Harris A / Borgnia MJ / Shi D / Bartesaghi A / He H / Pejchal R / Kang YK / Depetris R / Marozsan AJ / Sanders RW / Klasse PJ / Milne JL / Wilson IA / Olson WC / Moore JP / Subramaniam S
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures.
Authors: Audray Harris / Mario J Borgnia / Dan Shi / Alberto Bartesaghi / Haifeng He / Robert Pejchal / Yun Kenneth Kang / Rafael Depetris / Andre J Marozsan / Rogier W Sanders / Per Johan Klasse / ...Authors: Audray Harris / Mario J Borgnia / Dan Shi / Alberto Bartesaghi / Haifeng He / Robert Pejchal / Yun Kenneth Kang / Rafael Depetris / Andre J Marozsan / Rogier W Sanders / Per Johan Klasse / Jacqueline L S Milne / Ian A Wilson / William C Olson / John P Moore / Sriram Subramaniam /
Abstract: The initial step in HIV-1 infection occurs with the binding of cell surface CD4 to trimeric HIV-1 envelope glycoproteins (Env), a heterodimer of a transmembrane glycoprotein (gp41) and a surface ...The initial step in HIV-1 infection occurs with the binding of cell surface CD4 to trimeric HIV-1 envelope glycoproteins (Env), a heterodimer of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120). The design of soluble versions of trimeric Env that display structural and functional properties similar to those observed on intact viruses is highly desirable from the viewpoint of designing immunogens that could be effective as vaccines against HIV/AIDS. Using cryoelectron tomography combined with subvolume averaging, we have analyzed the structure of SOSIP gp140 trimers, which are cleaved, solubilized versions of the ectodomain of trimeric HIV-1 Env. We show that unliganded gp140 trimers adopt a quaternary arrangement similar to that displayed by native unliganded trimers on the surface of intact HIV-1 virions. When complexed with soluble CD4, Fab 17b, which binds to gp120 at its chemokine coreceptor binding site, or both soluble CD4 and 17b Fab, gp140 trimers display an open conformation in which there is an outward rotation and displacement of each gp120 protomer. We demonstrate that the molecular arrangements of gp120 trimers in the closed and open conformations of the soluble trimer are the same as those observed for the closed and open states, respectively, of trimeric gp120 on intact HIV-1 BaL virions, establishing that soluble gp140 trimers can be designed to mimic the quaternary structural transitions displayed by native trimeric Env.
History
DepositionJul 11, 2011-
Header (metadata) releaseMay 31, 2012-
Map releaseMay 31, 2012-
UpdateMay 31, 2012-
Current statusMay 31, 2012Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_5321.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with sCD4
Voxel sizeX=Y=Z: 4.1 Å
Density
Contour LevelBy AUTHOR: 2.3 / Movie #1: 2.3
Minimum - Maximum-8.26800632 - 10.20363998
Average (Standard dev.)-0.00153029 (±0.68582147)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 410.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z410.000410.000410.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-8.26810.204-0.002

-
Supplemental data

-
Sample components

-
Entire : SOSIP gp140 KNH1144 sCD4

EntireName: SOSIP gp140 KNH1144 sCD4
Components
  • Sample: SOSIP gp140 KNH1144 sCD4
  • Protein or peptide: SOSIP gp140 KNH1144 sCD4

-
Supramolecule #1000: SOSIP gp140 KNH1144 sCD4

SupramoleculeName: SOSIP gp140 KNH1144 sCD4 / type: sample / ID: 1000 / Oligomeric state: trimeric / Number unique components: 3

-
Macromolecule #1: SOSIP gp140 KNH1144 sCD4

MacromoleculeName: SOSIP gp140 KNH1144 sCD4 / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Human immunodeficiency virus 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF

-
Atomic model buiding 1

Initial modelPDB ID:
SoftwareName: Chimera
RefinementSpace: REAL

+
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