2B1H | pdb_00002b1h

Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with UG29 peptide

• PDB DOI: https://doi.org/10.2210/pdb2B1H/pdb

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


• Deposited: 2005-09-15 Released: 2006-07-04 
• Deposition Author(s): Stanfield, R.L., Gorny, M.K., Zolla-Pazner, S., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.238 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of human immunodeficiency virus type 1 (HIV-1) neutralizing antibody 2219 in complex with three different V3 peptides reveal a new binding mode for HIV-1 cross-reactivity.

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

(2006) J Virol 80: 6093-6105

• PubMed: 16731948 
• DOI: https://doi.org/10.1128/JVI.00205-06
• Primary Citation Related Structures: 
  2B0S, 2B1A, 2B1H


• PubMed Abstract: 
  

  Human monoclonal antibody 2219 is a neutralizing antibody isolated from a human immunodeficiency virus type 1-infected individual. 2219 was originally selected for binding to a V3 fusion protein and can neutralize primary isolates from subtypes B, A, and F. Thus, 2219 represents a cross-reactive, human anti-V3 antibody. Fab 2219 binds to one face of the variable V3 beta-hairpin, primarily contacting conserved residues on the N-terminal beta-strand of V3, leaving the V3 crown or tip largely accessible. Three V3/2219 complexes reveal the antibody-bound conformations for both the N- and C-terminal regions that flank the V3 crown and illustrate how twisting of the V3 loop alters the relative dispositions and pairing of the amino acids in the adjacent V3 beta-strands and how the antibody can accommodate V3 loops with different sequences.

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Organizational Affiliation: 
• Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content 

• Total Structure Weight: 49.7 kDa 
• Atom Count: 3,572 
• Modeled Residue Count: 457 
• Deposited Residue Count: 464 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 2219, light chain	A [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 2219, heavy chain	B [auth H]	226	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UG29 peptide of Exterior membrane glycoprotein GP120	C [auth P]	23	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.899	α = 90
b = 94.501	β = 90
c = 96.617	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-04 
Deposition Author(s): Stanfield, R.L., Gorny, M.K., Zolla-Pazner, S., Wilson, I.A.

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary