Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 49.63 kDa 
• Atom Count: 3660 
• Residue Count: 457 
• Unique protein chains: 3

2B0S

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

• DOI: 10.2210/pdb2B0S/pdb

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


• Deposited: 2005-09-14 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: 2.30 Å
• R-Value Free: 0.267 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

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: 10.1128/JVI.00205-06
• Primary Citation of Related Structures:  
  2B1H, 2B1A, 2B0S


• 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]

Macromolecules

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

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MN peptide of Exterior membrane glycoprotein GP120	P	19	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	H, L	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	H, L	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.267 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.471	α = 90
b = 60.471	β = 90
c = 275.194	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

• Deposited Date: 2005-09-14 
• 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: Advisory, Data collection, Refinement description