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- EMDB-20894: Negative-stain EM map from 3D sorting of BG505-immunized rhesus m... -

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Basic information

Entry
Database: EMDB / ID: EMD-20894
TitleNegative-stain EM map from 3D sorting of BG505-immunized rhesus macaque 11M-088 wk 12 serum fab complexed with BG505 SOSIP.664 trimer
Map dataNegative-stain EM map from 3D sorting of BG505-immunized rhesus macaque 11M-088 wk 12 serum fab complexed with BG505 SOSIP.664 trimer
Sample
  • Complex: Polyclonal serum fab with BG505 SOSIP.664
    • Complex: BG505 SOSIPv5.2 trimer
    • Complex: Polyclonal Fab
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / negative staining / Resolution: 25.5 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
DepositionOct 30, 2019-
Header (metadata) releaseNov 27, 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: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20894.png

Downloads & links

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Map

FileDownload / File: emd_20894.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative-stain EM map from 3D sorting of BG505-immunized rhesus macaque 11M-088 wk 12 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: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.03718919 - 0.11467512
Average (Standard dev.)0.0007436004 (±0.0071211504)
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/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.0370.1150.001

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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: BG505 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: BG505 SOSIPv5.2 trimer

SupramoleculeName: BG505 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: 180000
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3300
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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