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- EMDB-7906: Negative stain EM map of BG505 SOSIP.644 in complex with PG9 Fab ... -

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Basic information

Entry
Database: EMDB / ID: 7906
TitleNegative stain EM map of BG505 SOSIP.644 in complex with PG9 Fab and serum from rabbit 3417 PB1
Map dataNegative stain EM map of BG505 SOSIP.664 in complex with PG9 Fab and serum Fab from rabbit 3417 PB1
SampleComplex of BG505 SOSIP.664 with PG9 Fab and serum from rabbit 3417 PB1:
SourceHuman immunodeficiency virus
Methodsingle particle reconstruction / negative staining / 18.45 Å resolution
AuthorsTurner HL / Ward AB / Nogal B
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: 0.0367
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0367
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7906.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:0.0367 (by author), 0.0367 (movie #1):
Minimum - Maximum-0.06171277 - 0.11553654
Average (Standard dev.)0.00080505665 (0.009739771)
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-0.0620.1160.001

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Supplemental data

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Sample components

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Entire Complex of BG505 SOSIP.664 with PG9 Fab and serum from rabbit 3417 PB1

EntireName: Complex of BG505 SOSIP.664 with PG9 Fab and serum from rabbit 3417 PB1
Details: Complex was purified through SEC after adding excess PG9 and serum
Number of components: 1

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Component #1: protein, Complex of BG505 SOSIP.664 with PG9 Fab and serum from r...

ProteinName: Complex of BG505 SOSIP.664 with PG9 Fab and serum from rabbit 3417 PB1
Details: Complex was purified through SEC after adding excess PG9 and serum
Recombinant expression: No
SourceSpecies: Human immunodeficiency virus
Source (engineered)Expression System: Homo sapiens (human) / Strain: HEK293F

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.114 mg/ml / Buffer solution: TBS / pH: 7.4
Stainingat 2%
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: 438

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 7104
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 18.45 Å / Resolution method: FSC 0.5 CUT-OFF

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