3MLR

Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a NY5 V3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conserved structural elements in the V3 crown of HIV-1 gp120.

Jiang, X.Burke, V.Totrov, M.Williams, C.Cardozo, T.Gorny, M.K.Zolla-Pazner, S.Kong, X.P.

(2010) Nat.Struct.Mol.Biol. 17: 955-961

  • DOI: 10.1038/nsmb.1861
  • Primary Citation of Related Structures:  3GO1, 3MLS, 3MLT, 3MLU, 3MLV, 3MLW, 3MLX, 3MLY, 3MLZ

  • PubMed Abstract: 
  • Binding of the third variable region (V3) of the HIV-1 envelope glycoprotein gp120 to the cell-surface coreceptors CCR5 or CXCR4 during viral entry suggests that there are conserved structural elements in this sequence-variable region. These conserve ...

    Binding of the third variable region (V3) of the HIV-1 envelope glycoprotein gp120 to the cell-surface coreceptors CCR5 or CXCR4 during viral entry suggests that there are conserved structural elements in this sequence-variable region. These conserved elements could serve as epitopes to be targeted by a vaccine against HIV-1. Here we perform a systematic structural analysis of representative human anti-V3 monoclonal antibodies in complex with V3 peptides, revealing that the crown of V3 has four conserved structural elements: an arch, a band, a hydrophobic core and the peptide backbone. These are either unaffected by or are subject to minimal sequence variation. As these regions are targeted by cross-clade neutralizing human antibodies, they provide a blueprint for the design of vaccine immunogens that could elicit broadly cross-reactive protective antibodies.


    Organizational Affiliation

    Department of Biochemistry, New York University School of Medicine, New York, New York, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
L
219N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
H
226N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HIV-1 gp120 third variable region (V3) crown
P
20Human immunodeficiency virus type 1 group M subtype BGene Names: env
Find proteins for P12490 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12490
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.414α = 87.86
b = 43.076β = 85.50
c = 58.212γ = 85.82
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
ADSCdata collection
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-04-18 
  • Released Date: 2010-07-14 
  • Deposition Author(s): Kong, X.-P.

Revision History 

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description