2CJU

Crystal structure of the TEPC15-Vk45.1 anti-2-phenyl-5-oxazolone NQ16- 113.8 scFv in complex with phOxGABA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural Basis of Affinity Maturation of the Tepc15/V(Kappa)45.1 Anti-2-Phenyl-5-Oxazolone Antibodies.

Scotti, C.Gherardi, E.

(2006) J Mol Biol 359: 1161

  • DOI: https://doi.org/10.1016/j.jmb.2006.04.036
  • Primary Citation of Related Structures:  
    2CJU, 2UUD

  • PubMed Abstract: 

    Affinity maturation is a process that leads to the emergence of more efficient antibodies following initial antigen encounter and represents a key strategy of the adaptive immunity of vertebrate organisms. Earlier and detailed sequence studies of the antibody response to a model antigen, the hapten 2-phenyl-5-oxazolone (phOx), define three different classes of antibodies. Class I antibodies use the V(H)Ox1/V(kappa)Ox1 gene pair and dominate the early stages of the anti-phOx response, class II antibodies use the V(kappa)Ox1 gene but a different V(H) segment and are common in the intermediate stages, and class III antibodies use the TEPC15/V(kappa)45.1 genes and play the greatest role in the late stages. Only the crystal structure of one anti-phOx antibody, the class II NQ10/12.5 Fab fragment, has been described. Here we report the crystal structures of the scFv form of the low and high affinity anti-phOx class III antibodies NQ10/1.12 and NQ16/113.8 complexed with the hapten. The two antibodies differ by nine amino acid substitutions, all located in the V(H) domain. Analysis of the two structures shows that affinity maturation results from an increase in surface complementarity, as a consequence of a finely tuned and highly concerted process chaperoned by the somatic mutations, and implies a more efficient hapten-induced fit in the mature antibody. The data also demonstrate that class III antibodies respond in a completely different way to the architectural problem of binding phOx compared to the class II antibody NQ10/12.5.


  • Organizational Affiliation

    Dipartimento di Medicina Sperimentale, Universita' di Pavia, Italy. claudia.scotti@unipv.it


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NQ16-113.8 ANTI-PHOX ANTIBODYA [auth H]121Mus musculusMutation(s): 0 
UniProt
Find proteins for P01789 (Mus musculus)
Explore P01789 
Go to UniProtKB:  P01789
Entity Groups  
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UniProt GroupP01789
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NQ16-113.8 ANTI-PHOX ANTIBODYB [auth L]113Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PHX
Query on PHX

Download Ideal Coordinates CCD File 
C [auth H]4-{[(Z)-(5-OXO-2-PHENYL-1,3-OXAZOL-4(5H)-YLIDENE)METHYL]AMINO}BUTANOIC ACID
C14 H14 N2 O4
PXGNVFUWTUIRCJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.97α = 90
b = 74.19β = 90
c = 134.18γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKLdata reduction
HKLdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-10-16
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description