3P9W

Crystal structure of an engineered human autonomous VH Domain in complex with VEGF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Design of Synthetic Autonomous VH Domain Libraries and Structural Analysis of a VH Domain Bound to Vascular Endothelial Growth Factor.

Ma, X.Barthelemy, P.A.Rouge, L.Wiesmann, C.Sidhu, S.S.

(2013) J.Mol.Biol. 425: 2247-2259

  • DOI: 10.1016/j.jmb.2013.03.020

  • PubMed Abstract: 
  • We compared the capacity of an autonomous heavy chain variable (VH) domain (VH-B1a) to support diversity within its antigen-binding site relative to the conventional antigen-binding fragment (Fab) from which it was derived. We find that VH-B1a can to ...

    We compared the capacity of an autonomous heavy chain variable (VH) domain (VH-B1a) to support diversity within its antigen-binding site relative to the conventional antigen-binding fragment (Fab) from which it was derived. We find that VH-B1a can tolerate significant diversity within all three complementarity-determining regions (CDRs) and also within framework 3, and thus, VH-B1a and the Fab are similar in terms of the regions of the antigen-binding site that can tolerate diversity without compromising stability. We constructed libraries of synthetic VH domains and isolated binders with moderate affinity for vascular endothelial growth factor (VEGF) from a library in which only CDR3 was randomized. One binder was subjected to affinity maturation to derive an autonomous VH domain (VH-V1a) that recognized both human and mouse VEGF with high affinity (KD=16nM or 10nM, respectively). Structural analysis revealed that VH-V1a binds to an epitope that is distinct from the epitopes of a natural VEGF receptor and six different anti-VEGF Fabs. Moreover, VH-V1a recognizes VEGF by using an unusual paratope consisting predominantly of CDR3 but with significant contributions from framework residues within the former light chain interface. These results suggest that VH-B1a and other autonomous VH domains may be useful scaffolds to support both conventional libraries with antigen-binding sites built from the three CDR loops and, also, nonconventional libraries with antigen-binding sites built from CDR3 and the former light chain interface.


    Organizational Affiliation

    Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor A
A, C, E, G
106Homo sapiensMutation(s): 0 
Gene Names: VEGFA (VEGF)
Find proteins for P15692 (Homo sapiens)
Go to Gene View: VEGFA
Go to UniProtKB:  P15692
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
human VEGF
B, D, F, H
123N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.727α = 90.00
b = 132.908β = 90.00
c = 175.481γ = 90.00
Software Package:
Software NamePurpose
DNAdata collection
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-10-18 
  • Released Date: 2012-04-18 
  • Deposition Author(s): Ma, X., Wiesmann, C.

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-07-18
    Type: Other
  • Version 1.2: 2013-03-27
    Type: Database references
  • Version 1.3: 2013-04-03
    Type: Database references
  • Version 1.4: 2013-06-12
    Type: Database references
  • Version 1.5: 2013-06-19
    Type: Database references