3UJI

Crystal structure of anti-HIV-1 V3 Fab 2558 in complex with MN peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Human Anti-V3 HIV-1 Monoclonal Antibodies Encoded by the VH5-51/VL Lambda Genes Define a Conserved Antigenic Structure.

Gorny, M.K.Sampson, J.Li, H.Jiang, X.Totrov, M.Wang, X.H.Williams, C.O'Neal, T.Volsky, B.Li, L.Cardozo, T.Nyambi, P.Zolla-Pazner, S.Kong, X.P.

(2011) Plos One 6: e27780-e27780

  • DOI: 10.1371/journal.pone.0027780
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Preferential usage of immunoglobulin (Ig) genes that encode antibodies (Abs) against various pathogens is rarely observed and the nature of their dominance is unclear in the context of stochastic recombination of Ig genes. The hypothesis that restric ...

    Preferential usage of immunoglobulin (Ig) genes that encode antibodies (Abs) against various pathogens is rarely observed and the nature of their dominance is unclear in the context of stochastic recombination of Ig genes. The hypothesis that restricted usage of Ig genes predetermines the antibody specificity was tested in this study of 18 human anti-V3 monoclonal Abs (mAbs) generated from unrelated individuals infected with various subtypes of HIV-1, all of which preferentially used pairing of the VH5-51 and VL lambda genes. Crystallographic analysis of five VH5-51/VL lambda-encoded Fabs complexed with various V3 peptides revealed a common three dimensional (3D) shape of the antigen-binding sites primarily determined by the four complementarity determining regions (CDR) for the heavy (H) and light (L) chains: specifically, the H1, H2, L1 and L2 domains. The CDR H3 domain did not contribute to the shape of the binding pocket, as it had different lengths, sequences and conformations for each mAb. The same shape of the binding site was further confirmed by the identical backbone conformation exhibited by V3 peptides in complex with Fabs which fully adapted to the binding pocket and the same key contact residues, mainly germline-encoded in the heavy and light chains of five Fabs. Finally, the VH5-51 anti-V3 mAbs recognized an epitope with an identical 3D structure which is mimicked by a single mimotope recognized by the majority of VH5-51-derived mAbs but not by other V3 mAbs. These data suggest that the identification of preferentially used Ig genes by neutralizing mAbs may define conserved epitopes in the diverse virus envelopes. This will be useful information for designing vaccine immunogen inducing cross-neutralizing Abs.


    Organizational Affiliation

    Department of Pathology, New York University School of Medicine, New York, New York, United States of America. mirek.gorny@med.nyu.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Light chain of anti-HIV-1 V3 monoclonal antibody 2558
L
209N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab region of the heavy chain of anti-HIV-1 V3 monoclonal antibody 2558
H
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
P
23Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: env
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P05877
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
H
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.351α = 90.00
b = 73.097β = 121.98
c = 88.662γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data scaling
MAR345data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-11-07 
  • Released Date: 2011-12-28 
  • Deposition Author(s): Kong, X.P.

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description