1Q1J | pdb_00001q1j

Crystal Structure Analysis of anti-HIV-1 Fab 447-52D in complex with V3 peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.285 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 

Literature

Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447-52D.

Stanfield, R.L., Gorny, M.K., Williams, C., Zolla-Pazner, S., Wilson, I.A.

(2004) Structure 12: 193-204

  • DOI: https://doi.org/10.1016/j.str.2004.01.003
  • Primary Citation Related Structures: 
    1Q1J

  • PubMed Abstract: 

    447-52D is a human monoclonal antibody isolated from a heterohybridoma derived from an HIV-1-infected individual. This antibody recognizes the hypervariable gp120 V3 loop, and neutralizes both X4 and R5 primary isolates, making it one of the most effective anti-V3 antibodies characterized to date. The crystal structure of the 447-52D Fab in complex with a 16-mer V3 peptide at 2.5 A resolution reveals that the peptide beta hairpin forms a three-stranded mixed beta sheet with complementarity determining region (CDR) H3, with most of the V3 side chains exposed to solvent. Sequence specificity is conferred through interaction of the type-II turn (residues GPGR) at the apex of the V3 hairpin with the base of CDR H3. This novel mode of peptide-antibody recognition enables the antibody to bind to many different V3 sequences where only the GPxR core epitope is absolutely required.

    • Organizational Affiliation: 
    • Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 98.55 kDa 
  • Atom Count: 6,875 
  • Modeled Residue Count: 912 
  • Deposited Residue Count: 924 
  • Unique protein chains: 3

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 447-52D, light chainA [auth L],
D [auth M]		215Homo sapiensMutation(s): 0 
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 447-52D, heavy chainB [auth H],
E [auth I]		231Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
gp120 V3 peptideC [auth P],
F [auth Q]		16N/AMutation(s): 0 
UniProt
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B (isolate MN))
Explore P05877 
Go to UniProtKB:  P05877
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05877
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.285 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.673α = 90
b = 74.903β = 100.57
c = 100.047γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary