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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 dataBG505 SOSIP.664 in complex with rabbit Fab 43A2
Sample
  • Complex: BG505 SOSIP.664 in complex with rabbit Fab 43A2
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 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

emd_21498.png

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)
AnnotationBG505 SOSIP.664 in complex with rabbit Fab 43A2
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

Histogram

Histogram (log scale)
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
Components
  • Complex: BG505 SOSIP.664 in complex with rabbit Fab 43A2

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Supramolecule #1: BG505 SOSIP.664 in complex with rabbit Fab 43A2

SupramoleculeName: BG505 SOSIP.664 in complex with rabbit Fab 43A2 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 2878
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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