3L7F

Structure of IL-13 antibody H2L6, A humanized variant OF C836


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Human framework adaptation of a mouse anti-human IL-13 antibody.

Fransson, J.Teplyakov, A.Raghunathan, G.Chi, E.Cordier, W.Dinh, T.Feng, Y.Giles-Komar, J.Gilliland, G.Lollo, B.Malia, T.J.Nishioka, W.Obmolova, G.Zhao, S.Zhao, Y.Swanson, R.V.Almagro, J.C.

(2010) J Mol Biol 398: 214-231

  • DOI: https://doi.org/10.1016/j.jmb.2010.03.004
  • Primary Citation of Related Structures:  
    3L5W, 3L5X, 3L7F, 4PS4

  • PubMed Abstract: 

    Humanization of a potent neutralizing mouse anti-human IL-13 antibody (m836) using a method called human framework adaptation (HFA) is reported. HFA consists of two steps: human framework selection (HFS) and specificity-determining residue optimization (SDRO). The HFS step involved generation of a library of m836 antigen binding sites combined with diverse human germline framework regions (FRs), which were selected based on structural and sequence similarities between mouse variable domains and a repertoire of human antibody germline genes. SDRO consisted of diversifying specificity-determining residues and selecting variants with improved affinity using phage display. HFS of m836 resulted in a 5-fold loss of affinity, whereas SDRO increased the affinity up to 100-fold compared to the HFS antibody. Crystal structures of Fabs in complex with IL-13 were obtained for m836, the HFS variant chosen for SDRO, and one of the highest-affinity SDRO variants. Analysis of the structures revealed that major conformational changes in FR-H1 and FR-H3 occurred after FR replacement, but none of them had an evident direct impact on residues in contact with IL-13. Instead, subtle changes affected the V(L)/V(H) (variable-light domain/variable-heavy domain) interface and were likely responsible for the 5-fold decreased affinity. After SDRO, increased affinity resulted mainly from rearrangements in hydrogen-bonding pattern at the antibody/antigen interface. Comparison with m836 putative germline genes suggested interesting analogies between natural affinity maturation and the engineering process that led to the potent HFA anti-human IL-13 antibody.


  • Organizational Affiliation

    Centocor R&D, Inc., 3210 Merryfield Row, San Diego, CA 92121, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H2L6 LIGHT CHAINA [auth L],
C [auth A],
E [auth D]
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H2L6 HEAVY CHAINB [auth H],
D [auth B],
F [auth E]
224Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.64α = 90
b = 228.16β = 90
c = 234γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Derived calculations, Polymer sequence
  • Version 2.1: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description