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- EMDB-20396: Cryo-EM Reconstruction of Polyclonal Serum Fab From a Protected R... -

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Basic information

Entry
Database: EMDB / ID: EMD-20396
TitleCryo-EM Reconstruction of Polyclonal Serum Fab From a Protected Rhesus Macaque Complexed with BG505 SOSIP.664
Map dataPolyclonal Serum Fab From a Protected Rhesus Macaque Complexed with BG505 SOSIP.664
Sample
  • Complex: Polyclonal Fab complexed with BG505 SOSIP.664
    • Complex: Polyclonal Fab
    • Complex: BG505 SOSIP.664v5.2
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsNogal B / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI136621 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI100663 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 2, 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: 0.275
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.275
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6v0r
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6v0r
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20396.png

Downloads & links

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Map

FileDownload / File: emd_20396.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPolyclonal Serum Fab From a Protected Rhesus Macaque Complexed with BG505 SOSIP.664
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.275 / Movie #1: 0.275
Minimum - Maximum-1.9381598 - 3.1949768
Average (Standard dev.)-0.0012759729 (±0.08566497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.600329.600329.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.9383.195-0.001

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Supplemental data

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Sample components

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Entire : Polyclonal Fab complexed with BG505 SOSIP.664

EntireName: Polyclonal Fab complexed with BG505 SOSIP.664
Components
  • Complex: Polyclonal Fab complexed with BG505 SOSIP.664
    • Complex: Polyclonal Fab
    • Complex: BG505 SOSIP.664v5.2

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Supramolecule #1: Polyclonal Fab complexed with BG505 SOSIP.664

SupramoleculeName: Polyclonal Fab complexed with BG505 SOSIP.664 / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Polyclonal Fab

SupramoleculeName: Polyclonal Fab / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #3: BG505 SOSIP.664v5.2

SupramoleculeName: BG505 SOSIP.664v5.2 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1

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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

BufferpH: 7
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155394
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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