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- EMDB-7896: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3... -

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Entry
Database: EMDB / ID: 7896
TitleHIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
Map dataHIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
SampleHIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1:
(Envelope glycoprotein ...) x 2 / (Monoclonal antibody 10A ...) x 2 / (ligand) x 3
Function / homologyImmunoglobulin subtype / Gp120 core superfamily / Immunoglobulin-like fold / Immunoglobulin C1-set / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Immunoglobulin-like domain superfamily / Envelope glycoprotein Gp160 / Immunoglobulin V-set domain / Envelope glycoprotein GP120 ...Immunoglobulin subtype / Gp120 core superfamily / Immunoglobulin-like fold / Immunoglobulin C1-set / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Immunoglobulin-like domain superfamily / Envelope glycoprotein Gp160 / Immunoglobulin V-set domain / Envelope glycoprotein GP120 / Retroviral envelope protein / Immunoglobulin C1-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / host cell endosome membrane / evasion or tolerance by virus of host immune response / antigen binding / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / integral component of membrane / identical protein binding / IgG heavy chain VDJ region / Ig kappa-b4 chain C region / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Function and homology information
SourceHomo sapiens (human) / Human immunodeficiency virus 1 / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / 4.71 Å resolution
AuthorsTurner HL / Cottrell CA / Oyen D / Wilson IA / Ward AB
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.
Validation ReportPDB-ID: 6did

SummaryFull reportAbout validation report
DateDeposition: May 23, 2018 / Header (metadata) release: Jul 4, 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: 0.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6did
  • Surface level: 0.35
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7896.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:0.35 (by author), 0.35 (movie #1):
Minimum - Maximum-0.40159664 - 1.3945129
Average (Standard dev.)0.0036196986 (0.060318965)
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-0.4021.3950.004

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Supplemental data

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Sample components

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Entire HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3...

EntireName: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
Details: Model includes fitted atomic structures for HIV Env BG505 SOSIP (PDB ID: 5v8m) and 10A Fab (PDB ID: 6cjk).
Number of components: 8

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Component #1: protein, HIV Env BG505 SOSIP with polyclonal Fabs from immunized ...

ProteinName: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
Details: Model includes fitted atomic structures for HIV Env BG505 SOSIP (PDB ID: 5v8m) and 10A Fab (PDB ID: 6cjk).
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: protein, Envelope glycoprotein gp160

ProteinName: Envelope glycoprotein gp160 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 54.064277 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Envelope glycoprotein gp160

ProteinName: Envelope glycoprotein gp160 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 17.146482 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Monoclonal antibody 10A light chain

ProteinName: Monoclonal antibody 10A light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 23.047424 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Monoclonal antibody 10A heavy chain

ProteinName: Monoclonal antibody 10A heavy chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 22.263018 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 93 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #7: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #8: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 39 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5.6 mg/ml / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 52.6 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 2500.0 nm
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: C3 (3 fold cyclic) / Number of projections: 161639
3D reconstructionResolution: 4.71 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

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