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

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Basic information

Entry
Database: EMDB / ID: EMD-0466
TitleHIV-1 Env State 2A
Map dataEnvelope
Sample
  • Complex: HIV-1 Env in complex with BNM-III-170, A32 and 17b antibodies
Biological speciesHuman 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 ...Alsahafi 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 / ...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.
History
DepositionJan 15, 2019-
Header (metadata) releaseJan 30, 2019-
Map releaseMay 1, 2019-
UpdateMay 1, 2019-
Current statusMay 1, 2019Processing site: RCSB / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0466.png

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)
AnnotationEnvelope
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

Histogram

Histogram (log scale)
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
Components
  • Complex: HIV-1 Env in complex with BNM-III-170, A32 and 17b antibodies

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

SupramoleculeName: HIV-1 Env in complex with BNM-III-170, A32 and 17b antibodies
type: complex / ID: 1 / Parent: 0
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.
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: HIV-1 BAL/SuPT1-CCR5 CL.30
Recombinant expressionOrganism: Human immunodeficiency virus 1 / Recombinant strain: HIV-1 BAL/SuPT1-CCR5 CL.30

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.335 mg/mL
BufferpH: 7.2
Component:
ConcentrationName
0.01 MTris-HCl
0.1 MNaCl
1.0 mMEDTA
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2000.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsLot#P4311

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number real images: 1033 / Average electron dose: 1.4 e/Å2
Details: 1033 was the number of initial images (movies) that 1032 were selected for particle picking
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.2076 µm / Calibrated defocus min: 1.1559 µm / Calibrated magnification: 79000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

DetailsCollected movies aligned using motioncorr protocol
Particle selectionNumber selected: 14076
Details: The initial number of extracted particles (200*200)
CTF correctionSoftware: (Name: CTFFIND (ver. 4), RELION (ver. 2))
Details: Using CTFFind4 to estimate the CTF and corrected for CTF in refinement with Relion-auto-refine
Startup modelType of model: NONE
Details: The initial model obtained firstly by Relion-initial-map protocol and 3000 particles. Then using 4000 particles a more accurate map achieved by "highres protocol" (Scipion).
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 13.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2)
Details: The resolution obtained using gold-standard method by Relion-auto-refine
Number images used: 10597
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Details: Initial angular assignment achieved by Relion 2D classification and alignment protocol.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2) / Details: After processing the data by Relion-auto-refine

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