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- EMDB-7555: CryoEM map of BG505 SOSIP.664 in complex with post boost 1 serum ... -

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Basic information

Entry
Database: EMDB / ID: 7555
TitleCryoEM map of BG505 SOSIP.664 in complex with post boost 1 serum from rabbit 3417
Map dataBG505 SOSIP.664 in complex with serum from rabbit 3417 post boost 1. Map of antibodies bound to trimer after several rounds of 3D classification in CryoSparc.
SampleComplex of BG505 SOSIP.664 and serum antibodies from post boost 1 from rabbit 3417. Subset of particles from dataset.:
SourceHuman immunodeficiency virus
Methodsingle particle reconstruction / cryo EM / 4.7 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: Mar 13, 2018 / Header (metadata) release: Apr 18, 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: 0.381
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.381
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7555.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.15 Å/pix.
= 345. Å
300 pix
1.15 Å/pix.
= 345. Å
300 pix
1.15 Å/pix.
= 345. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density
Contour Level:0.381 (by author), 0.381 (movie #1):
Minimum - Maximum-0.31383744 - 1.1800797
Average (Standard dev.)0.0032141434 (0.061049055)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.0.0.
Limit299.299.299.
Spacing300300300
CellA=B=C: 345.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z345.000345.000345.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.3141.1800.003

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Supplemental data

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Sample components

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Entire Complex of BG505 SOSIP.664 and serum antibodies from post boost 1...

EntireName: Complex of BG505 SOSIP.664 and serum antibodies from post boost 1 from rabbit 3417. Subset of particles from dataset.
Details: Serum was purified through SEC after using a Protein A or G column to capture complex then cleave IgG releasing Fab and trimer. Substoichiometric occupancy and flexibility show lack of density in Fab region while trimer core is refined to higher resolution. Map shows strong density of single Fab bound to glycan hole and low densities of Fabs bound to the trimer base.
Number of components: 1

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Component #1: protein, Complex of BG505 SOSIP.664 and serum antibodies from pos...

ProteinName: Complex of BG505 SOSIP.664 and serum antibodies from post boost 1 from rabbit 3417. Subset of particles from dataset.
Details: Serum was purified through SEC after using a Protein A or G column to capture complex then cleave IgG releasing Fab and trimer. Substoichiometric occupancy and flexibility show lack of density in Fab region while trimer core is refined to higher resolution. Map shows strong density of single Fab bound to glycan hole and low densities of Fabs bound to the trimer base.
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: cryo EM
Sample solutionSpecimen conc.: 1.44 mg/ml / Buffer solution: TBS / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 14274
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF

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