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- EMDB-21498: BG505 SOSIP.664 in complex with rabbit Fab 43A2 -

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Basic information

Entry
Database: EMDB / ID: EMD-21498
TitleBG505 SOSIP.664 in complex with rabbit Fab 43A2
Map data
SampleBG505 SOSIP.664 in complex with rabbit Fab 43A2
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / Resolution: 25 Å
AuthorsCottrell CA / Shin M / Ward AB
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F31 AI131873 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
CitationJournal: Sci Adv / Year: 2020
Title: HIV envelope trimer-elicited autologous neutralizing antibodies bind a region overlapping the N332 glycan supersite.
Authors: Bartek Nogal / Laura E McCoy / Marit J van Gils / Christopher A Cottrell / James E Voss / Raiees Andrabi / Matthias Pauthner / Chi-Hui Liang / Terrence Messmer / Rebecca Nedellec / Mia Shin ...Authors: Bartek Nogal / Laura E McCoy / Marit J van Gils / Christopher A Cottrell / James E Voss / Raiees Andrabi / Matthias Pauthner / Chi-Hui Liang / Terrence Messmer / Rebecca Nedellec / Mia Shin / Hannah L Turner / Gabriel Ozorowski / Rogier W Sanders / Dennis R Burton / Andrew B Ward /
Abstract: To date, immunization studies of rabbits with the BG505 SOSIP.664 HIV envelope glycoprotein trimers have revealed the 241/289 glycan hole as the dominant neutralizing antibody epitope. Here, we ...To date, immunization studies of rabbits with the BG505 SOSIP.664 HIV envelope glycoprotein trimers have revealed the 241/289 glycan hole as the dominant neutralizing antibody epitope. Here, we isolated monoclonal antibodies from a rabbit that did not exhibit glycan hole-dependent autologous serum neutralization. The antibodies did not compete with a previously isolated glycan hole-specific antibody but did compete with N332 glycan supersite broadly neutralizing antibodies. A 3.5-Å cryoEM structure of one of the antibodies in complex with the BG505 SOSIP.v5.2 trimer demonstrated that while the epitope recognized overlapped the N332 glycan supersite by contacting the GDIR motif at the base of V3, primary contacts were located in the variable V1 loop. These data suggest that strain-specific responses to V1 may interfere with broadly neutralizing responses to the N332 glycan supersite and vaccine immunogens may require engineering to minimize these off-target responses or steer them toward a more desirable pathway.
History
DepositionMar 1, 2020-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateJul 1, 2020-
Current statusJul 1, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21498.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 192 pix.
= 380.16 Å
1.98 Å/pix.
x 192 pix.
= 380.16 Å
1.98 Å/pix.
x 192 pix.
= 380.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.98 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.042042617 - 0.068289325
Average (Standard dev.)0.00020493027 (±0.004324318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 380.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.981.981.98
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z380.160380.160380.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0420.0680.000

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Supplemental data

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Sample components

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Entire BG505 SOSIP.664 in complex with rabbit Fab 43A2

EntireName: BG505 SOSIP.664 in complex with rabbit Fab 43A2 / Number of components: 1

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Component #1: protein, BG505 SOSIP.664 in complex with rabbit Fab 43A2

ProteinName: BG505 SOSIP.664 in complex with rabbit Fab 43A2 / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293F

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle
Sample solutionpH: 7.4
VitrificationCryogen name: NONE

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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: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI CETA (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 2878
3D reconstructionSoftware: RELION / Resolution: 25 Å / Resolution method: FSC 0.143 CUT-OFF

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