Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.63 kDa 
• Atom Count: 4119 
• Residue Count: 460 
• Unique protein chains: 3

3UJJ

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

• DOI: 10.2210/pdb3UJJ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Mutation(s): No 


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

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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 

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

• PubMed: 22164215 
• DOI: 10.1371/journal.pone.0027780
• Structures With Same Primary Citation


• 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.

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Organizational Affiliation: 

Department of Pathology, New York University School of Medicine, New York, New York, United States of America. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Light chain of anti-HIV-1 V3 monoclonal antibody 4025	L	213	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fab region of the heavy chain of anti-HIV-1 V3 monoclonal antibody 4025	H	230	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Gp120	P	23	Human immunodeficiency virus 1	Mutation(s): 0
Find proteins for Q9Q714 (Human immunodeficiency virus type 1 group M subtype H (isolate VI991)) Explore Q9Q714  Go to UniProtKB:  Q9Q714

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H, L	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H, L	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	H, L, P	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 = 136.143	α = 90
b = 136.143	β = 90
c = 73.411	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History 

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