6DID

HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization.

Bianchi, M.Turner, H.L.Nogal, B.Cottrell, C.A.Oyen, D.Pauthner, M.Bastidas, R.Nedellec, R.McCoy, L.E.Wilson, I.A.Burton, D.R.Ward, A.B.Hangartner, L.

(2018) Immunity 49: 288-300.e8

  • DOI: 10.1016/j.immuni.2018.07.009
  • Structures With Same Primary Citation

  • PubMed 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 barrier to fully understanding the humoral response to 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.


    Organizational Affiliation

    Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: lhangart@scripps.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Monoclonal antibody 10A heavy chain
D, K, L
214Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A1Y1B8B1 (Oryctolagus cuniculus)
Go to UniProtKB:  A0A1Y1B8B1
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
A, F, G
481Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
B, I, J
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S7 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S7
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Monoclonal antibody 10A light chain
C, E, H
217Oryctolagus cuniculusMutation(s): 0 
Find proteins for P01840 (Oryctolagus cuniculus)
Go to UniProtKB:  P01840
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, F, G, I, J
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
A, F, G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
A, F, G
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 AI100663
Bill & Melinda Gates FoundationUnited StatesOPP1115782

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence