Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 49.97 kDa 
• Atom Count: 3321 
• Residue Count: 436 
• Unique protein chains: 3

3DRO

Crystal structure of the HIV-1 Cross Neutralizing Antibody 2F5 in complex with gp41 Peptide ELLELDKWASLWN grown in ammonium sulfate

• DOI: 10.2210/pdb3DRO/pdb

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


• Deposited: 2008-07-11 Released: 2008-07-29 
• Deposition Author(s): Julien, J.-P., Bryson, S., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free: 0.263 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

Literature

Structural details of HIV-1 recognition by the broadly neutralizing monoclonal antibody 2F5: epitope conformation, antigen-recognition loop mobility, and anion-binding site.

Julien, J.P., Bryson, S., Nieva, J.L., Pai, E.F.

(2008) J Mol Biol 384: 377-392

• PubMed: 18824005 
• DOI: 10.1016/j.jmb.2008.09.024
• Structures With Same Primary Citation


• PubMed Abstract: 
  

2F5 is a monoclonal antibody with potent and broadly neutralizing activity against HIV-1. It targets the membrane-proximal external region (MPER) of the gp41 subunit of the envelope glycoprotein and interferes with the process of fusion between viral and host cell membranes. This study presents eight 2F5 F(ab)' crystal structures in complex with various gp41 peptide epitopes. These structures reveal several key features of this antibody-antigen interaction. (1) Whenever free of contacts caused by crystal artifacts, the extended complementarity-determining region H3 loop is mobile; this is true for ligand-free and epitope-bound forms. (2) The interaction between the antibody and the gp41 ELDKWA epitope core is absolutely critical, and there are also close and specific contacts with residues located N-terminal to the epitope core. (3) Residues located at the C-terminus of the gp41 ELDKWA core do not interact as tightly with the antibody. However, in the presence of a larger peptide containing the gp41 fusion peptide segment, these residues adopt a conformation consistent with the start of an alpha-helix. (4) At high sulfate concentrations, the electron density maps of 2F5 F(ab)'-peptide complexes contain a peak that may mark a binding site for phosphate groups of negatively charged lipid headgroups. The refined atomic-level details of 2F5 paratope-epitope interactions revealed here should contribute to a better understanding of the mechanism of 2F5-based virus neutralization, in general, and prove important for the design of potential vaccine candidates intended to elicit 2F5-like antibody production.

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Organizational Affiliation: 

Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
2F5 Fab heavy chain	B	235	Homo sapiens	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
2F5 Fab light chain	A	214	Homo sapiens	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
ELLELDKWASLWN gp41 peptide	P	13	N/A	Mutation(s): 0
Find proteins for Q5S532 (Human immunodeficiency virus 1) Go to UniProtKB:  Q5S532

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free: 0.263 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.9	α = 90
b = 76.5	β = 90
c = 93.9	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345dtb	data collection
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-07-11 
• Released Date: 2008-07-29 
Deposition Author(s): Julien, J.-P., Bryson, S., Pai, E.F.

Revision History 

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-02-08
  Changes: Other