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- EMDB-0466: HIV-1 Env State 2A -

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Entry
Database: EMDB / ID: EMD-0466
TitleHIV-1 Env State 2A
Map data
SampleHIV-1 Env in complex with BNM-III-170, A32 and 17b antibodies
SourceHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 13.08 Å
AuthorsAlsahafi N / Bakouche N / Kazemi M / Richard J / Ding S / Bhattacharyya S / Das D / Anand SP / Prevost J / Tolbert WD / Lu H / Medjahed H / Delgado GGO / Kirk S / Melillo B / Mothes W / Sodroski J / Smith III AB / Kaufmann DE / Wu X / Pazgier M / Rouiller I / Finzi A / Munro JB
CitationJournal: Cell Host Microbe / Year: 2019
Title: An Asymmetric Opening of HIV-1 Envelope Mediates Antibody-Dependent Cellular Cytotoxicity.
Authors: Nirmin Alsahafi / Nordine Bakouche / Mohsen Kazemi / Jonathan Richard / Shilei Ding / Sudipta Bhattacharyya / Durba Das / Sai Priya Anand / Jérémie Prévost / William D Tolbert / Hong Lu / Halima Medjahed / Gabrielle Gendron-Lepage / Gloria Gabrielle Ortega Delgado / Sharon Kirk / Bruno Melillo / Walther Mothes / Joseph Sodroski / Amos B Smith / Daniel E Kaufmann / Xueling Wu / Marzena Pazgier / Isabelle Rouiller / Andrés Finzi / James B Munro /
Abstract: The HIV-1 envelope glycoprotein (Env) (gp120-gp41) is the target for neutralizing antibodies and antibody-dependent cellular cytotoxicity (ADCC). HIV-1 Env is flexible, sampling different ...The HIV-1 envelope glycoprotein (Env) (gp120-gp41) is the target for neutralizing antibodies and antibody-dependent cellular cytotoxicity (ADCC). HIV-1 Env is flexible, sampling different conformational states. Before engaging CD4, Env adopts a closed conformation (State 1) that is largely antibody resistant. CD4 binding induces an intermediate state (State 2), followed by an open conformation (State 3) that is susceptible to engagement by antibodies that recognize otherwise occluded epitopes. We investigate conformational changes in Env that induce ADCC in the presence of a small-molecule CD4-mimetic compound (CD4mc). We uncover an asymmetric Env conformation (State 2A) recognized by antibodies targeting the conserved gp120 inner domain and mediating ADCC. Sera from HIV+ individuals contain these antibodies, which can stabilize Env State 2A in combination with CD4mc. Additionally, triggering State 2A on HIV-infected primary CD4 T cells exposes epitopes that induce ADCC. Strategies that induce this Env conformation may represent approaches to fight HIV-1 infection.
DateDeposition: Jan 15, 2019 / Header (metadata) release: Jan 30, 2019 / Map release: May 1, 2019 / Update: May 1, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0246
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0246
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0466.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 200 pix.
= 340. Å
1.7 Å/pix.
x 200 pix.
= 340. Å
1.7 Å/pix.
x 200 pix.
= 340. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
Density
Contour LevelBy AUTHOR: 0.0246 / Movie #1: 0.0246
Minimum - Maximum-0.6560266 - 0.623866
Average (Standard dev.)-0.00458397 (±0.022168187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 340.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.71.71.7
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z340.000340.000340.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.6560.624-0.005

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Supplemental data

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Sample components

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Entire HIV-1 Env in complex with BNM-III-170, A32 and 17b antibodies

EntireName: HIV-1 Env in complex with BNM-III-170, A32 and 17b antibodies
Details: HIV-1 Env present on the surface of Aldrithiol-2 (AT-2)-inactivated HIV-1 particles incubated with BNM-III-170, A32 and 17b antibodies.
Number of components: 1

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Component #1: protein, HIV-1 Env in complex with BNM-III-170, A32 and 17b antibodies

ProteinName: HIV-1 Env in complex with BNM-III-170, A32 and 17b antibodies
Details: HIV-1 Env present on the surface of Aldrithiol-2 (AT-2)-inactivated HIV-1 particles incubated with BNM-III-170, A32 and 17b antibodies.
Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1 / Strain: HIV-1 BAL/SuPT1-CCR5 CL.30
Source (engineered)Expression System: Human immunodeficiency virus 1 / Strain: HIV-1 BAL/SuPT1-CCR5 CL.30

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.335 mg/mL / pH: 7.2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 79000.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1033
Details: 1033 was the number of initial images (movies) that 1032 were selected for particle picking

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 10597 / Details: Collected movies aligned using motioncorr protocol
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION
CTF correction: Using CTFFind4 to estimate the CTF and corrected for CTF in refinement with Relion-auto-refine
Resolution: 13.08 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The resolution obtained using gold-standard method by Relion-auto-refine
Euler angles: After processing the data by Relion-auto-refine

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