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- EMDB-7887: Negative Stain EM map of polyclonal serum in complex with BG505 S... -

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Entry
Database: EMDB / ID: 7887
TitleNegative Stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from rabbit 3418 at post boost 2
Map dataNegative stain EM map of serum in complex with BG505 SOSIP.664 from rabbit 3418 after post boost 2
SampleNegative Stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from rabbit 3418 at post boost 2:
SourceOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / 20 Å resolution
AuthorsWard AB / Turner HL
CitationJournal: Immunity / Year: 2018
Title: Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization.
Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton / Andrew B Ward / Lars Hangartner
Abstract: Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a ...Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a barrier to fully understanding the humoral response to antigens and hinders rational vaccine design efforts. Here, we describe a method of characterizing polyclonal responses by using electron microscopy, and we applied this method to the immunization of rabbits with an HIV-1 envelope glycoprotein vaccine candidate, BG505 SOSIP.664. We detected known epitopes within the polyclonal sera and revealed how antibody responses evolved during the prime-boosting strategy to ultimately result in a neutralizing antibody response. We uncovered previously unidentified epitopes, including an epitope proximal to one recognized by human broadly neutralizing antibodies as well as potentially distracting non-neutralizing epitopes. Our method provides an efficient and semiquantitative map of epitopes that are targeted in a polyclonal antibody response and should be of widespread utility in vaccine and infection studies.
DateDeposition: May 23, 2018 / Header (metadata) release: Jun 20, 2018 / Map release: Sep 5, 2018 / Last update: Sep 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7887.map.gz (map file in CCP4 format, 11944 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
144 pix
2.05 Å/pix.
= 295.2 Å
144 pix
2.05 Å/pix.
= 295.2 Å
144 pix
2.05 Å/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
Contour Level:0.022 (by author), 0.022 (movie #1):
Minimum - Maximum-0.03935943 - 0.107288145
Average (Standard dev.)0.00022518891 (0.006861736)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions144144144
Origin0.0.0.
Limit143.143.143.
Spacing144144144
CellA=B=C: 295.19998 Å
α=β=γ: 90.0 deg.

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/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.0390.1070.000

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Supplemental data

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Sample components

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Entire Negative Stain EM map of polyclonal serum in complex with BG505 S...

EntireName: Negative Stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from rabbit 3418 at post boost 2
Number of components: 1

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Component #1: protein, Negative Stain EM map of polyclonal serum in complex wit...

ProteinName: Negative Stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from rabbit 3418 at post boost 2
Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionSpecimen conc.: 0.136 mg/ml / pH: 7.4
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 109

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 17487
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.5 CUT-OFF

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