|Entry||Database: PDB / ID: 6did|
|Title||HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1|
|Keywords||VIRAL PROTEIN / HIV / antibodies / antibody|
|Function / homology||Retroviral envelope protein GP41-like / Gp120 core superfamily / Immunoglobulin C1-set / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Immunoglobulin-like domain / Immunoglobulin subtype / Envelope glycoprotein Gp160 ...Retroviral envelope protein GP41-like / Gp120 core superfamily / Immunoglobulin C1-set / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Immunoglobulin-like domain / Immunoglobulin subtype / Envelope glycoprotein Gp160 / Envelope glycoprotein GP120 / Retroviral envelope protein / Immunoglobulin C1-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization / host cell endosome membrane / evasion or tolerance by virus of host immune response / viral protein processing / antigen binding / fusion of virus membrane with host plasma membrane / 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
|Specimen source||Human immunodeficiency virus 1|
Oryctolagus cuniculus (rabbit)
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.71 Å resolution|
|Authors||Turner, H.L. / Cottrell, C.A. / Oyen, D. / Wilson, I.A. / Ward, A.B.|
|Citation||Journal: 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.
SummaryFull reportAbout validation report
|Date||Deposition: May 23, 2018 / Release: Sep 5, 2018|
|Structure viewer||Molecule: |
Downloads & links
A: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
F: Envelope glycoprotein gp160
I: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
J: Envelope glycoprotein gp160
C: Monoclonal antibody 10A light chain
D: Monoclonal antibody 10A heavy chain
E: Monoclonal antibody 10A light chain
K: Monoclonal antibody 10A heavy chain
H: Monoclonal antibody 10A light chain
L: Monoclonal antibody 10A heavy chain
-Envelope glycoprotein ... , 2 types, 6 molecules A
F G B I J
Mass: 54064.277 Da / Num. of mol.: 3 / Fragment: GP120 domain residues 30-505 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
Mass: 17146.482 Da / Num. of mol.: 3 / Fragment: GP41 domain residues 509-661 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S7
-Monoclonal antibody 10A ... , 2 types, 6 molecules C
E H D K L
Mass: 23047.424 Da / Num. of mol.: 3 / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human) / References: UniProt: P01840
Mass: 22263.018 Da / Num. of mol.: 3 / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human) / References: UniProt: A0A1Y1B8B1
-Non-polymers , 3 types, 147 molecules
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: 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).
Entity ID: 1,
|Source (natural)||Organism: Homo sapiens (human)||Source (recombinant)||Organism: Homo sapiens (human)||Buffer solution||pH: 7.4||Specimen||Conc.: 5.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES||Specimen support||Grid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R1.2/1.3||Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TALOS ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 8.5 sec. / Electron dose: 52.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|Image scans||Width: 3710 / Height: 3838 / Movie frames/image: 34|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Number of particles selected: 170078|
|Symmetry||Point symmetry: C3|
|3D reconstruction||Resolution: 4.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 161639 / Symmetry type: POINT|
|Atomic model building||Ref protocol: RIGID BODY FIT / Ref space: REAL|
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