3QYC

Structure of a dimeric anti-HER2 single domain antibody

• PDB DOI: https://doi.org/10.2210/pdb3QYC/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-03 Released: 2012-02-08 
• Deposition Author(s): Baral, T.N., Chao, S., Li, S., Tanha, J., Arbabai, M., Wang, S., Zhang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.229 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

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

• PubMed: 22253912 
• DOI: https://doi.org/10.1371/journal.pone.0030149
• Primary Citation of Related Structures:  
  3QYC


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.48 kDa 
• Atom Count: 2,096 
• Modelled Residue Count: 248 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VH domain of IgG molecule	A, B	146	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.229 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.805	α = 90
b = 76.989	β = 90
c = 81.358	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-08 
Deposition Author(s): Baral, T.N., Chao, S., Li, S., Tanha, J., Arbabai, M., Wang, S., Zhang, J.

Revision History  

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