Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 98.55 kDa 
• Atom Count: 6875 
• Residue Count: 912 
• Unique protein chains: 3

1Q1J

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

• DOI: 10.2210/pdb1Q1J/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2003-07-21 Released: 2004-02-17 
• Deposition Author(s): Stanfield, R.L., Gorny, M.K., Williams, C., Zolla-Pazner, S., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.285 
• R-Value Work: 0.250 
• R-Value Observed: 0.250 

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

• PubMed: 14962380 
• DOI: 10.1016/j.str.2004.01.003
• Primary Citation of 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 447-52D, light chain	L, M	215	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 447-52D, heavy chain	H, I	231	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
gp120 V3 peptide	P, Q	16	N/A	Mutation(s): 0
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B (isolate MN)) Explore P05877  Go to UniProtKB:  P05877

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.285 
• R-Value Work: 0.250 
• R-Value Observed: 0.250 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.673	α = 90
b = 74.903	β = 100.57
c = 100.047	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-07-21 
• Released Date: 2004-02-17 
Deposition Author(s): Stanfield, R.L., Gorny, M.K., Williams, C., Zolla-Pazner, S., Wilson, I.A.

Revision History 

• 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