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- EMDB-20399: Unimmunized control rhesus macaque BZ05 (challenged with SHIV) se... -

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Basic information

Entry
Database: EMDB / ID: EMD-20399
TitleUnimmunized control rhesus macaque BZ05 (challenged with SHIV) serum fab complexed with BG505 SOSIP.664 trimer
Map dataUnimmunized control rhesus macaque BZ05 (challenged with SHIV) serum fab complexed with BG505 SOSIP.664 trimer
Sample
  • Complex: Polyclonal serum fab with BG505 SOSIP.664
    • Complex: SOSIPv5.2 trimer
    • Complex: Polyclonal Fab
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / negative staining / Resolution: 16.4 Å
AuthorsNogal B / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteAI136621 United States
National Institutes of Health/National Human Genome Research InstituteAI100663 United States
CitationJournal: Cell Rep / Year: 2020
Title: Mapping Polyclonal Antibody Responses in Non-human Primates Vaccinated with HIV Env Trimer Subunit Vaccines.
Authors: Bartek Nogal / Matteo Bianchi / Christopher A Cottrell / Robert N Kirchdoerfer / Leigh M Sewall / Hannah L Turner / Fangzhu Zhao / Devin Sok / Dennis R Burton / Lars Hangartner / Andrew B Ward /
Abstract: Rational immunogen design aims to focus antibody responses to vulnerable sites on primary antigens. Given the size of these antigens, there is, however, potential for eliciting unwanted, off-target ...Rational immunogen design aims to focus antibody responses to vulnerable sites on primary antigens. Given the size of these antigens, there is, however, potential for eliciting unwanted, off-target responses. Here, we use our electron microscopy polyclonal epitope mapping approach to describe the antibody specificities elicited by immunization of non-human primates with soluble HIV envelope trimers and subsequent repeated viral challenge. An increased diversity of epitopes recognized and the approach angle by which these antibodies bind constitute a hallmark of the humoral response in most protected animals. We also show that fusion peptide-specific antibodies are likely responsible for some neutralization breadth. Moreover, cryoelectron microscopy (cryo-EM) analysis of a fully protected animal reveals a high degree of clonality within a subset of putatively neutralizing antibodies, enabling a detailed molecular description of the antibody paratope. Our results provide important insights into the immune response against a vaccine candidate that entered into clinical trials in 2019.
History
DepositionJul 3, 2019-
Header (metadata) releaseDec 4, 2019-
Map releaseApr 1, 2020-
UpdateApr 1, 2020-
Current statusApr 1, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0183
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0183
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20399.png

Downloads & links

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Map

FileDownload / File: emd_20399.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnimmunized control rhesus macaque BZ05 (challenged with SHIV) serum fab complexed with BG505 SOSIP.664 trimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 144 pix.
= 295.2 Å		2.05 Å/pix.
x 144 pix.
= 295.2 Å		2.05 Å/pix.
x 144 pix.
= 295.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0183 / Movie #1: 0.0183
Minimum - Maximum-0.052790646 - 0.09172507
Average (Standard dev.)0.00039448796 (±0.00764149)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 295.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z295.200295.200295.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.0530.0920.000

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Supplemental data

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Sample components

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Entire : Polyclonal serum fab with BG505 SOSIP.664

EntireName: Polyclonal serum fab with BG505 SOSIP.664
Components
  • Complex: Polyclonal serum fab with BG505 SOSIP.664
    • Complex: SOSIPv5.2 trimer
    • Complex: Polyclonal Fab

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Supramolecule #1: Polyclonal serum fab with BG505 SOSIP.664

SupramoleculeName: Polyclonal serum fab with BG505 SOSIP.664 / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: SOSIPv5.2 trimer

SupramoleculeName: SOSIPv5.2 trimer / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: unidentified (others)

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Supramolecule #3: Polyclonal Fab

SupramoleculeName: Polyclonal Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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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: 4.5
StainingType: NEGATIVE / Material: uranyl formate
GridDetails: unspecified

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: OTHER / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 78442
Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9543
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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