Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

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This is version 1.3 of the entry. See complete history


The 2.0-A resolution crystal structure of a trimeric antibody fragment with noncognate VH-VL domain pairs shows a rearrangement of VH CDR3.

Pei, X.Y.Holliger, P.Murzin, A.G.Williams, R.L.

(1997) Proc Natl Acad Sci U S A 94: 9637-9642

  • DOI: https://doi.org/10.1073/pnas.94.18.9637
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The 2.0-A resolution x-ray crystal structure of a novel trimeric antibody fragment, a "triabody," has been determined. The trimer is made up of polypeptides constructed in a manner identical to that previously described for some "diabodies": a VL domain directly fused to the C terminus of a VH domain-i.e., without any linker sequence. The trimer has three Fv heads with the polypeptides arranged in a cyclic, head-to-tail fashion. For the particular structure reported here, the polypeptide was constructed with a VH domain from one antibody fused to the VL domain from an unrelated antibody giving rise to "combinatorial" Fvs upon formation of the trimer. The structure shows that the exchange of the VL domain from antibody B1-8, a Vlambda domain, with the VL domain from antibody NQ11, a Vkappa domain, leads to a dramatic conformational change in the VH CDR3 loop of antibody B1-8. The magnitude of this change is similar to the largest of the conformational changes observed in antibody fragments in response to antigen binding. Combinatorial pairing of VH and VL domains constitutes a major component of antibody diversity. Conformationally flexible antigen-binding sites capable of adapting to the specific CDR3 loop context created upon VH-VL pairing may be employed by the immune system to maximize the structural diversity of the immune response.

  • Organizational Affiliation

    Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B [auth C]
256Mus musculusMutation(s): 0 
Gene Names: B1-8 VH DOMAIN FUSED TO NQ11 V
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.32α = 90
b = 136.32β = 90
c = 74.8γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-08-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Database references, Refinement description