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- EMDB-13333: HIV-1 Env (BG505 SOSIP.664) in complex with the bNAb 7-155 -

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Basic information

Entry
Database: EMDB / ID: EMD-13333
TitleHIV-1 Env (BG505 SOSIP.664) in complex with the bNAb 7-155
Map data
Sample
  • Complex: HIV Env trimer (BG505 SOSIP.664 T332N) with one 7-155 Fab per protomer
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsBontems F / Fernandez I / Pehau-Arnaudet G / Rey F
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Exp Med / Year: 2022
Title: Epitope convergence of broadly HIV-1 neutralizing IgA and IgG antibody lineages in a viremic controller.
Authors: Valérie Lorin / Ignacio Fernández / Guillemette Masse-Ranson / Mélanie Bouvin-Pley / Luis M Molinos-Albert / Cyril Planchais / Thierry Hieu / Gérard Péhau-Arnaudet / Dominik Hrebík / ...Authors: Valérie Lorin / Ignacio Fernández / Guillemette Masse-Ranson / Mélanie Bouvin-Pley / Luis M Molinos-Albert / Cyril Planchais / Thierry Hieu / Gérard Péhau-Arnaudet / Dominik Hrebík / Giulia Girelli-Zubani / Oriane Fiquet / Florence Guivel-Benhassine / Rogier W Sanders / Bruce D Walker / Olivier Schwartz / Johannes F Scheid / Jordan D Dimitrov / Pavel Plevka / Martine Braibant / Michael S Seaman / François Bontems / James P Di Santo / Félix A Rey / Hugo Mouquet /
Abstract: Decrypting the B cell ontogeny of HIV-1 broadly neutralizing antibodies (bNAbs) is paramount for vaccine design. Here, we characterized IgA and IgG bNAbs of three distinct B cell lineages in a ...Decrypting the B cell ontogeny of HIV-1 broadly neutralizing antibodies (bNAbs) is paramount for vaccine design. Here, we characterized IgA and IgG bNAbs of three distinct B cell lineages in a viremic controller, two of which comprised only IgG+ or IgA+ blood memory B cells; the third combined both IgG and IgA clonal variants. 7-269 bNAb in the IgA-only lineage displayed the highest neutralizing capacity despite limited somatic mutation, and delayed viral rebound in humanized mice. bNAbs in all three lineages targeted the N332 glycan supersite. The 2.8-Å resolution cryo-EM structure of 7-269-BG505 SOSIP.664 complex showed a similar pose as 2G12, on an epitope mainly composed of sugar residues comprising the N332 and N295 glycans. Binding and cryo-EM structural analyses showed that antibodies from the two other lineages interact mostly with glycans N332 and N386. Hence, multiple B cell lineages of IgG and IgA bNAbs focused on a unique HIV-1 site of vulnerability can codevelop in HIV-1 viremic controllers.
History
DepositionAug 5, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateMar 16, 2022-
Current statusMar 16, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13333.png

Downloads & links

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Map

FileDownload / File: emd_13333.map.gz / Format: CCP4 / Size: 40.6 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 Å/pix.
x 220 pix.
= 440. Å		2 Å/pix.
x 220 pix.
= 440. Å		2 Å/pix.
x 220 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.035683382 - 0.19453426
Average (Standard dev.)6.2287414e-05 (±0.0079500135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z440.000440.000440.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0360.1950.000

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Supplemental data

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Sample components

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Entire : HIV Env trimer (BG505 SOSIP.664 T332N) with one 7-155 Fab per protomer

EntireName: HIV Env trimer (BG505 SOSIP.664 T332N) with one 7-155 Fab per protomer
Components
  • Complex: HIV Env trimer (BG505 SOSIP.664 T332N) with one 7-155 Fab per protomer

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Supramolecule #1: HIV Env trimer (BG505 SOSIP.664 T332N) with one 7-155 Fab per protomer

SupramoleculeName: HIV Env trimer (BG505 SOSIP.664 T332N) with one 7-155 Fab per protomer
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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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

Concentration0.2 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
10.0 mMTris
75.0 mMSodium ChlorideNaCl
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 284 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

CTF correctionSoftware - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54361
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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