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- EMDB-21412: Ligand-free HIV envelope glycoprotein on AT-2 treated BaL strain virus -

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Basic information

Entry
Database: EMDB / ID: EMD-21412
TitleLigand-free HIV envelope glycoprotein on AT-2 treated BaL strain virus
Map dataLigand-free HIV envelope glycoprotein on AT-2 treated BaL strain virus
Sample
  • Complex: HIV gp120-gp41 trimer
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 11.5 Å
AuthorsJun L / Ze L / Li W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM134775 United States
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Subnanometer structures of HIV-1 envelope trimers on aldrithiol-2-inactivated virus particles.
Authors: Ze Li / Wenwei Li / Maolin Lu / Julian Bess / Cara W Chao / Jason Gorman / Daniel S Terry / Baoshan Zhang / Tongqing Zhou / Scott C Blanchard / Peter D Kwong / Jeffrey D Lifson / Walther Mothes / Jun Liu /
Abstract: The HIV-1 envelope glycoprotein (Env) trimer, composed of gp120 and gp41 subunits, mediates viral entry into cells. Recombinant Env trimers have been studied structurally, but characterization of Env ...The HIV-1 envelope glycoprotein (Env) trimer, composed of gp120 and gp41 subunits, mediates viral entry into cells. Recombinant Env trimers have been studied structurally, but characterization of Env embedded in intact virus membranes has been limited to low resolution. Here, we deploy cryo-electron tomography and subtomogram averaging to determine the structures of Env trimers on aldrithiol-2 (AT-2)-inactivated virions in ligand-free, antibody-bound and CD4-bound forms at subnanometer resolution. Tomographic reconstructions document molecular features consistent with high-resolution structures of engineered soluble and detergent-solubilized Env trimers. One of three conformational states previously predicted by smFRET was not observed by cryo-ET, potentially owing to AT-2 inactivation. We did observe Env trimers to open in situ in response to CD4 binding, with an outward movement of gp120-variable loops and an extension of a critical gp41 helix. Overall features of Env trimer embedded in AT-2-treated virions appear well-represented by current engineered trimers.
History
DepositionFeb 19, 2020-
Header (metadata) releaseMar 18, 2020-
Map releaseJul 1, 2020-
UpdateAug 19, 2020-
Current statusAug 19, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.19
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.19
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21412.png

Downloads & links

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Map

FileDownload / File: emd_21412.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLigand-free HIV envelope glycoprotein on AT-2 treated BaL strain virus
Voxel sizeX=Y=Z: 2.2 Å
Density
Contour LevelBy AUTHOR: 0.19 / Movie #1: 0.19
Minimum - Maximum-0.18240221 - 0.71352315
Average (Standard dev.)0.00013150259 (±0.056702074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-205-205-205
NX/NY/NZ411411411
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.1820.7140.000

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Supplemental data

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Sample components

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Entire : HIV gp120-gp41 trimer

EntireName: HIV gp120-gp41 trimer
Components
  • Complex: HIV gp120-gp41 trimer

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Supramolecule #1: HIV gp120-gp41 trimer

SupramoleculeName: HIV gp120-gp41 trimer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BaL strain

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 70 / Number images used: 15085
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: OTHER / Number subtomograms used: 13577

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