3MLS

Crystal structure of anti-HIV-1 V3 mAb 2557 Fab in complex with a HIV-1 gp120 V3 mimotope

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.216 

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This is version 1.3 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: https://doi.org/10.1038/nsmb.1861
  • Primary Citation of Related Structures:  
    3GO1, 3MLR, 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chainA [auth L],
D [auth M],
G [auth N],
J [auth O]		219Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chainB [auth H],
E [auth I],
H [auth J],
K		226Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Rationally designed V3 mimotopeC [auth P],
F [auth Q],
I [auth R],
L [auth S]		20N/AMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.746α = 90
b = 43.051β = 94.2
c = 274.341γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-11-27
    Changes: Data collection, Database references, Structure summary