2XQB

Crystal Structure of anti-IL-15 Antibody in Complex with human IL-15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Engineering a High Affinity Anti-Il-15 Antibody: Crystal Structure Reveals an Alpha-Helix in Vh Cdr3 as Key Component of Paratope.

Lowe, D.C.Gerhardt, S.Ward, A.Hargreaves, D.Anderson, M.Ferraro, F.Pauptit, R.A.Pattison, D.V.Buchanan, C.Popovic, B.Finch, D.K.Wilkinson, T.Sleeman, M.Vaughan, T.J.Mallinder, P.R.

(2011) J.Mol.Biol. 406: 160

  • DOI: 10.1016/j.jmb.2010.12.017

  • PubMed Abstract: 
  • Interleukin (IL) 15 is an inflammatory cytokine that plays an essential role in the activation, proliferation, and maintenance of specific natural killer cell and T-cell populations, and has been implicated as a mediator of inflammatory diseases. An ...

    Interleukin (IL) 15 is an inflammatory cytokine that plays an essential role in the activation, proliferation, and maintenance of specific natural killer cell and T-cell populations, and has been implicated as a mediator of inflammatory diseases. An anti-IL-15 antibody that blocked IL-15-dependent cellular responses was isolated by phage display and optimised via mutagenesis of the third complementarity-determining regions (CDRs) of variable heavy (VH) and variable light chains. Entire repertoires of improved variants were recombined with each other to explore the maximum potential sequence space. DISC0280, the most potent antibody isolated using this comprehensive strategy, exhibits a 228-fold increase in affinity and a striking 40,000-fold increase in cellular potency compared to its parent. Such a wholesale recombination strategy therefore represents a useful method for exploiting synergistic potency gains as part of future antibody engineering efforts. The crystal structure of DISC0280 Fab (fragment antigen binding), in complex with human IL-15, was determined in order to map the structural epitope and paratope. The most remarkable feature revealed lies within the paratope and is a novel six-amino-acid α-helix that sits within the VH CDR3 loop at the center of the antigen binding site. This is the first report to describe an α-helix as a principal component of a naturally derived VH CDR3 following affinity maturation.


    Organizational Affiliation

    MedImmune Ltd., Milstein Building, Granta Park, Cambridge CB1 6GH, UK. lowed@medimmune.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INTERLEUKIN 15
A
114Homo sapiensMutation(s): 0 
Gene Names: IL15
Find proteins for P40933 (Homo sapiens)
Go to Gene View: IL15
Go to UniProtKB:  P40933
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTI-IL-15 ANTIBODY
H
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ANTI-IL-15 ANTIBODY
L
211N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 185.186α = 90.00
b = 43.754β = 95.95
c = 70.087γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata scaling
d*TREKdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection, Source and taxonomy