[English] 日本語
Yorodumi
- EMDB-25178: Sub-tomogram averaged structure of HIV-1 Envelope protein in nati... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25178
TitleSub-tomogram averaged structure of HIV-1 Envelope protein in native membrane
Map data
Sample
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-L-fucopyranose
KeywordsHIV-1 / envelope protein / glycoprotein / Env / membrane bound / VIRAL PROTEIN
Function / homology
Function and homology information


: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 9.1 Å
AuthorsMangala Prasad V / Lee KK
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI140868 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM099989 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI143563 United States
CitationJournal: Cell / Year: 2022
Title: Cryo-ET of Env on intact HIV virions reveals structural variation and positioning on the Gag lattice.
Authors: Vidya Mangala Prasad / Daniel P Leaman / Klaus N Lovendahl / Jacob T Croft / Mark A Benhaim / Edgar A Hodge / Michael B Zwick / Kelly K Lee /
Abstract: HIV-1 Env mediates viral entry into host cells and is the sole target for neutralizing antibodies. However, Env structure and organization in its native virion context has eluded detailed ...HIV-1 Env mediates viral entry into host cells and is the sole target for neutralizing antibodies. However, Env structure and organization in its native virion context has eluded detailed characterization. Here, we used cryo-electron tomography to analyze Env in mature and immature HIV-1 particles. Immature particles showed distinct Env positioning relative to the underlying Gag lattice, providing insights into long-standing questions about Env incorporation. A 9.1-Å sub-tomogram-averaged reconstruction of virion-bound Env in conjunction with structural mass spectrometry revealed unexpected features, including a variable central core of the gp41 subunit, heterogeneous glycosylation between protomers, and a flexible stalk that allows Env tilting and variable exposure of neutralizing epitopes. Together, our results provide an integrative understanding of HIV assembly and structural variation in Env antigen presentation.
History
DepositionOct 20, 2021-
Header (metadata) releaseMar 9, 2022-
Map releaseMar 9, 2022-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.77
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.77
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ska
  • Surface level: 2.77
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25178.png

Downloads & links

-
Map

FileDownload / File: emd_25178.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.58 Å/pix.
x 120 pix.
= 309.6 Å		2.58 Å/pix.
x 120 pix.
= 309.6 Å		2.58 Å/pix.
x 120 pix.
= 309.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.77 / Movie #1: 2.77
Minimum - Maximum-12.714874 - 30.607009999999999
Average (Standard dev.)0.00078440865 (±0.9893365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 309.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.582.582.58
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z309.600309.600309.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-12.71530.6070.001

-
Supplemental data

-
Sample components

-
Entire : Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Components
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-L-fucopyranose

-
Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Env glycoprotein displayed on surface of HIV-1 / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Molecular weightTheoretical: 430 KDa

-
Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 52.170992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KLWVTVYYGV PVWKEATTTL FCASDAKAYD TEVHNVWATH ACVPTDPNPQ EVVLENVTEN FNMWKNNMVE QMHEDIISLW DQSLKPCVK LTPLCVTLNC TDLRNVTNIN NSSEGMRGEI KNCSFNITTS IRDKVKKDYA LFYRLDVVPI DNDNTSYRLI N CNTSTITQ ...String:
KLWVTVYYGV PVWKEATTTL FCASDAKAYD TEVHNVWATH ACVPTDPNPQ EVVLENVTEN FNMWKNNMVE QMHEDIISLW DQSLKPCVK LTPLCVTLNC TDLRNVTNIN NSSEGMRGEI KNCSFNITTS IRDKVKKDYA LFYRLDVVPI DNDNTSYRLI N CNTSTITQ ACPKVSFEPI PIHYCTPAGF AILKCKDKKF NGTGPCKNVS TVQCTHGIRP VVSTQLLLNG SLAEEEVVIR SS NFTDNAK NIIVQLKESV EINCTRPNNN TRKSIHIGPG RAFYTTGEII GDIRQAHCNI SRTKWNNTLN QIATKLKEQF GNN KTIVFN QSSGGDPEIV MHSFNCGGEF FYCNSTQLFN STWNFNGTWN LTQSNGTEGN DTITLPCRIK QIINMWQEVG KAMY APPIR GQIRCSSNIT GLILTRDGGT NSSGSEIFRP GGGDMRDNWR SELYKYKVVK IEPLGVAPTK

UniProtKB: Envelope glycoprotein gp160

-
Macromolecule #2: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 16.420559 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GFLGAAGSTM GAASMTLTVQ ARQLLSGIVQ QQNNLLRAIE AQQHLLQLTV WGIRQLQARV LAVERYLRDQ QLLGIWGCSG KLICTTAVP WNASWSNKSL EQIWNNMTWM EWDREINNYT SLIHSLIEEA QNQQEKNEQE LLELD

UniProtKB: Envelope glycoprotein gp160

-
Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 21 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #13: alpha-L-fucopyranose

MacromoleculeName: alpha-L-fucopyranose / type: ligand / ID: 13 / Number of copies: 3 / Formula: FUC
Molecular weightTheoretical: 164.156 Da
Chemical component information

ChemComp-FUC:
alpha-L-fucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Component - Concentration: 1.0 X / Component - Name: Phosphate buffer saline
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 58000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 32802
ExtractionNumber tomograms: 423 / Number images used: 63592 / Method: volumes picked semi-automatically
CTF correctionSoftware - Name: EMAN2 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: OTHER / Software - Name: EMAN2
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6ulc


Chain - Source name: PDB / Chain - Initial model type: experimental model
Details6ulc model was rigid body fitted into EM map. The flexible terminal Gp41 stalk region alone was fitted into density using COOT
RefinementProtocol: RIGID BODY FIT
Output model

PDB-7ska:
Sub-tomogram averaged structure of HIV-1 Envelope protein in native membrane

+
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