3QYC

Structure of a dimeric anti-HER2 single domain antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of a Human Single Domain Antibody Dimer Formed through V(H)-V(H) Non-Covalent Interactions.

Baral, T.N.Chao, S.Y.Li, S.Tanha, J.Arbabi-Ghahroudi, M.Zhang, J.Wang, S.

(2012) Plos One 7: e30149-e30149

  • DOI: 10.1371/journal.pone.0030149

  • PubMed Abstract: 
  • Single-domain antibodies (sdAbs) derived from human V(H) are considered to be less soluble and prone to aggregate which makes it difficult to determine the crystal structures. In this study, we isolated and characterized two anti-human epidermal grow ...

    Single-domain antibodies (sdAbs) derived from human V(H) are considered to be less soluble and prone to aggregate which makes it difficult to determine the crystal structures. In this study, we isolated and characterized two anti-human epidermal growth factor receptor-2 (HER2) sdAbs, Gr3 and Gr6, from a synthetic human V(H) phage display library. Size exclusion chromatography and surface plasmon resonance analyses demonstrated that Gr3 is a monomer, but that Gr6 is a strict dimer. To understand this different molecular behavior, we solved the crystal structure of Gr6 to 1.6 Å resolution. The crystal structure revealed that the homodimer assembly of Gr6 closely mimics the V(H)-V(L) heterodimer of immunoglobulin variable domains and the dimerization interface is dominated by hydrophobic interactions.


    Organizational Affiliation

    Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VH domain of IgG molecule
A, B
146N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.805α = 90.00
b = 76.989β = 90.00
c = 81.358γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Source and taxonomy