5V6M

Crystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A3 in complex with V3 peptide ConB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Increased epitope complexity correlated with antibody affinity maturation and a novel binding mode revealed by structures of rabbit antibodies against the third variable loop (V3) of HIV-1 gp120.

Pan, R.Qin, Y.Banasik, M.Lees, W.Shepherd, A.J.Cho, M.W.Kong, X.P.

(2018) J. Virol. --: --

  • DOI: 10.1128/JVI.01894-17
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The third variable (V3) loop of HIV-1 gp120 is an immunodominant region targeted by neutralizing antibodies (nAbs). Despite limited breadth, better characterization of the structural details of the interactions between these nAbs and their target epi ...

    The third variable (V3) loop of HIV-1 gp120 is an immunodominant region targeted by neutralizing antibodies (nAbs). Despite limited breadth, better characterization of the structural details of the interactions between these nAbs and their target epitopes would enhance our understanding of the mechanism of neutralization and facilitate designing better immunogens to induce nAbs with greater breadth. Recently, we isolated two anti-V3 neutralizing monoclonal antibodies (MAbs), 10A3 and 10A37, from a rabbit immunized with gp120 of the M group consensus sequence. In this study, crystal structures of these MAbs bound to target epitopes were determined. 10A3 binds to the V3 crown ( 303 TRKSIHIGPGRAF 317 ) using the cradle binding mode, similar to human V3 MAbs encoded by IGHV5-51 germ line genes, and its epitope structure resembles that bound to the human antibodies. In contrast, 10A37, which exhibits greater breadth and potency than 10A3, binds the V3 crown and the succeeding stem region ( 308 HIGPGRAFYTTGEI 323 ). Unexpectedly, the 315 RAFYTT 320 portion of the epitope existed as helical turns, a V3 structure that has not been observed previously. Its main chain-dominated antigen-antibody interactions not only explain the broad neutralization of 10A37 but also show that its epitope is a potential vaccine target to be further evaluated. In conclusion, our study provides novel insights about neutralization-susceptible epitope structures of the V3 loop of HIV-1 gp120 and demonstrates that, despite low amino acid sequence similarity to human antibody germ line genes, rabbits can serve as a useful animal model to evaluate human vaccine candidates. IMPORTANCE The apex crown of V3 of HIV-1 gp120 is the most immunogenic region of the surface glycoprotein, and many MAbs targeting this region have been developed. Structural understanding of V3 crown MAbs not only can help understand how antibody responses target this unique region but also contribute to immunogen design for vaccine development. We present here crystal structures of two neutralizing V3 MAbs, 10A3 and 10A37, developed from a rabbit immunized with gp120. Our analysis of 10A3 in complex with V3 provided a detailed example of how epitope complexity can evolve with affinity maturation, while that of 10A37 revealed a novel V3 binding mode targeting the C-terminal side of the V3 crown and showed that this region can form a helical structure. Our study provides novel insights about neutralization-susceptible V3 epitope structures and demonstrates that rabbits can serve as a useful animal model to evaluate human vaccine candidates.


    Organizational Affiliation

    Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom.,Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, New York, USA mcho@iastate.edu xiangpeng.kong@med.nyu.edu.,Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, New York, USA.,Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA mcho@iastate.edu xiangpeng.kong@med.nyu.edu.,Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A3
L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A3
H
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp120 V3 peptide of Con B sequence
P
15Human immunodeficiency virus type 1 group M subtype B (isolate JRCSF)Mutation(s): 0 
Gene Names: env
Find proteins for P20871 (Human immunodeficiency virus type 1 group M subtype B (isolate JRCSF))
Go to UniProtKB:  P20871
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 62.846α = 90.00
b = 83.870β = 90.00
c = 90.610γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXmodel building
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-03-17 
  • Released Date: 2018-01-17 
  • Deposition Author(s): Pan, R., Kong, X.-P.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI074286
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI100151

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2019-01-30
    Type: Data collection, Database references