3UJJ

Crystal structure of anti-HIV-1 V3 Fab 4025 in complex with Con A peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1371/journal.pone.0027780
  • Primary Citation of Related Structures:  
    3UJI, 3UJJ

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of anti-HIV-1 V3 monoclonal antibody 4025A [auth L]213Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab region of the heavy chain of anti-HIV-1 V3 monoclonal antibody 4025B [auth H]230Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gp120C [auth P]23Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q9Q714 (Human immunodeficiency virus type 1 group M subtype H (isolate VI991))
Explore Q9Q714 
Go to UniProtKB:  Q9Q714
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Q714
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
FA [auth H]
GA [auth H]
L
M [auth L]
N [auth L]
FA [auth H],
GA [auth H],
L,
M [auth L],
N [auth L],
O [auth L],
P [auth L],
Q [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth H]
BA [auth H]
CA [auth H]
D [auth L]
DA [auth H]
AA [auth H],
BA [auth H],
CA [auth H],
D [auth L],
DA [auth H],
E [auth L],
EA [auth H],
F [auth L],
G [auth L],
H [auth L],
I [auth L],
J [auth L],
K [auth L],
U [auth H],
V [auth H],
W [auth H],
X [auth H],
Y [auth H],
Z [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
HA [auth H]
IA [auth H]
JA [auth H]
KA [auth P]
R [auth L]
HA [auth H],
IA [auth H],
JA [auth H],
KA [auth P],
R [auth L],
S [auth L],
T [auth L]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.143α = 90
b = 136.143β = 90
c = 73.411γ = 120
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description