3BQU

Crystal Structure of the 2F5 Fab'-3H6 Fab Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.276 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the complex between the F(ab)' fragment of the cross-neutralizing anti-HIV-1 antibody 2F5 and the F(ab) fragment of its anti-idiotypic antibody 3H6.

Bryson, S.Julien, J.P.Isenman, D.E.Kunert, R.Katinger, H.Pai, E.F.

(2008) J.Mol.Biol. 382: 910-919

  • DOI: 10.1016/j.jmb.2008.07.057

  • PubMed Abstract: 
  • The monoclonal antibody 2F5 neutralizes a broad range of human immunodeficiency virus-1 isolates via a conserved epitope on the viral glycoprotein gp41. The conformation of the principal epitope is a type I beta-turn centered on gp41 residues (664)DK ...

    The monoclonal antibody 2F5 neutralizes a broad range of human immunodeficiency virus-1 isolates via a conserved epitope on the viral glycoprotein gp41. The conformation of the principal epitope is a type I beta-turn centered on gp41 residues (664)DKW(666); in addition, binding studies indicate that residues N- and C-terminal to this core as well as structurally more distant parts of gp41 also contribute to the interaction. Ab2/3H6 is an anti-idiotypic antibody that inhibits the interaction between 2F5 and gp41 and as such, Ab2/3H6 may, in principle, possess a paratope that mimics the gp41 epitope. To establish the potential of Ab2/3H6 to serve as a guide for the design of vaccine components against human immunodeficiency virus, we investigated the crystal structure of the heterodimeric complex of Ab2/3H6 F(ab) and 2F5 F(ab)'. Ab2/3H6 F(ab) binds to 2F5 F(ab)' via a helix-like protrusion formed by residues (58(H))RYSPSLNTRL(67(H)) of the 2F5 F(ab)' variable domain and proximal to but not overlapping with the gp41 (664)DKW(666) epitope-binding pocket. This defines Ab2/3H6 as an anti-idiotypic antibody of the Ab2gamma class, i.e., an antigen-inhibitable idiotype that does not carry the internal image of the linear primary gp41 (662)ELDKWAS(668) epitope.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2F5 Fab' light chain
A
214N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
2F5 Fab' heavy chain
B
235Homo sapiens
Find proteins for Q6PYX1 (Homo sapiens)
Go to UniProtKB:  Q6PYX1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
3H6 Fab light chain
C
233Mus musculusGene Names: Igkc (Igk-C)
Find proteins for A2NHM3 (Mus musculus)
Go to UniProtKB:  A2NHM3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
3H6 Fab heavy chain
D
241Mus musculus
Find proteins for P01756 (Mus musculus)
Go to UniProtKB:  P01756
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.276 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.440α = 90.00
b = 98.330β = 90.00
c = 154.390γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance