1VGE

TR1.9 FAB FRAGMENT OF A HUMAN IGG1 KAPPA AUTOANTIBODY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural studies of human autoantibodies. Crystal structure of a thyroid peroxidase autoantibody Fab.

Chacko, S.Padlan, E.A.Portolano, S.McLachlan, S.M.Rapoport, B.

(1996) J Biol Chem 271: 12191-12198

  • DOI: 10.1074/jbc.271.21.12191
  • Primary Citation of Related Structures:  
    1VGE

  • PubMed Abstract: 
  • The three-dimensional structure of the Fab of TR1.9, a high-affinity IgG1, kappa human autoantibody to thyroid peroxidase, was determined crystallographically to a resolution of 2.0 A. The combining site was found to be relatively flat, like other antibodies to large proteins ...

    The three-dimensional structure of the Fab of TR1.9, a high-affinity IgG1, kappa human autoantibody to thyroid peroxidase, was determined crystallographically to a resolution of 2.0 A. The combining site was found to be relatively flat, like other antibodies to large proteins. Sequence differences from the most closely related germline genes mainly occur at positions occupied by residues with outward-pointing side chains. An increased deformability of the second and third complementarity-determining regions of the heavy chain may result from the replacement of two germline asparagines and the presence of several glycines, and may allow "induced fit" in the binding to antigen. Four exposed charged residues, resulting from the use of a particular D (diversity) and J (joining) segments in the assembly of the heavy chain, may contribute to the high affinity of antigen binding. The crystal structure of TR1.9 Fab is the first for a human IgG high-affinity autoantibody.


    Organizational Affiliation

    Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20895-0560, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TR1.9 FABA [auth L]214Homo sapiensMutation(s): 0 
Gene Names: CDNA DERIVED FROM
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TR1.9 FABB [auth H]225Homo sapiensMutation(s): 0 
Gene Names: CDNA DERIVED FROMIGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens)
Explore P01857 
Go to UniProtKB:  P01857
PHAROS:  P01857
GTEx:  ENSG00000211896 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01857
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.926α = 90
b = 62.776β = 107.19
c = 84.79γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
X-PLORrefinement
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-06-10
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance