2UUD

Crystal structure of the TEPC15-Vk45.1 anti-2-phenyl-5-oxazolone NQ10- 1.12 scFv in complex with the hapten


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

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This is version 1.2 of the entry. See complete history


Literature

Structural Basis of Affinity Maturation of the Tepc15-Vkappa45.1 Anti-2-Phenyl-5-Oxazolone Antibodies

Scotti, C.Gherardi, E.

(2006) J Mol Biol 359: 1161

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

  • 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NQ10-1.12 ANTI-PHOX ANTIBODYHJ121Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NQ10-1.12 ANTI-PHOX ANTIBODYKL113Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NQ10-1.12 ANTI-PHOX ANTIBODYST18Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHX
Query on PHX

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.944α = 90
b = 75.657β = 111.33
c = 52.854γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2007-03-02 
  • Released Date: 2007-04-03 
  • Deposition Author(s): Scotti, C., Gherardi, E.
  • This entry supersedes: 2CJV

Revision History 

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance