1ETZ

THE THREE-DIMENSIONAL STRUCTURE OF AN ANTI-SWEETENER FAB, NC10.14, SHOWS THE EXTENT OF STRUCTURAL DIVERSITY IN ANTIGEN RECOGNITION BY IMMUNOGLOBULINS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The three-dimensional structure of a complex of a murine Fab (NC10. 14) with a potent sweetener (NC174): an illustration of structural diversity in antigen recognition by immunoglobulins.

Guddat, L.W.Shan, L.Broomell, C.Ramsland, P.A.Fan, Z.Anchin, J.M.Linthicum, D.S.Edmundson, A.B.

(2000) J Mol Biol 302: 853-872

  • DOI: 10.1006/jmbi.2000.4083
  • Primary Citation of Related Structures:  
    1ETZ

  • PubMed Abstract: 
  • The three-dimensional structure of a complex of an Fab from a murine IgG2b(lambda) antibody (NC10.14) with a high potency sweet tasting hap- ten, N-(p-cyanophenyl)-N'-(diphenylmethyl)-N"-(carboxymethyl)guan idine (NC174), has been determined to 2.6 A ...

    The three-dimensional structure of a complex of an Fab from a murine IgG2b(lambda) antibody (NC10.14) with a high potency sweet tasting hap- ten, N-(p-cyanophenyl)-N'-(diphenylmethyl)-N"-(carboxymethyl)guan idine (NC174), has been determined to 2.6 A resolution by X-ray crystallography. This complex crystallized in the triclinic space group P1, with two molecules in the asymmetric unit. In contrast to a companion monoclonal antibody (NC6.8) with a kappa-type light chain and similar high affinity for the NC174 ligand, the NC10.14 antibody possessed a large and deep antigen combining site bounded primarily by the third complementarity-determining regions (CDR3s) of the light and heavy chains. CDR3 of the heavy chain dominated the site and its crown protruded into the external solvent as a type 1' beta-turn. NC174 was nested against HCDR3 and was held in place by two tryptophan side-chains (L91 and L96) from LCDR3. The diphenyl rings were accommodated on an upper tier of the binding pocket that is largely hydrophobic. At the floor of the site, a positively charged arginine side-chain (H95) stabilized the orientation of the electronegative cyano group of the hapten. The negative charge on the acetate group was partially neutralized by a hydrogen bond with the phenolic hydroxyl group of tyrosine H58. Comparisons of the modes of binding of NC174 to the NC6.8 and NC10.14 antibodies illustrate the enormous structural and mechanistic diversity manifest by immune responses.


    Related Citations: 
    • Local and Transmitted Conformational Changes on Complexation of an Anti-sweetener Fab
      Guddat, L.W., Shan, L., Anchin, J.M., Linthicum, D.S., Edmundson, A.B.
      (1994) J Mol Biol 236: 247

    Organizational Affiliation

    Crystallography Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FAB NC10.14 - LIGHT CHAINAL215Mus musculusMutation(s): 0 
Find proteins for G0YP42 (Mus musculus)
Explore G0YP42 
Go to UniProtKB:  G0YP42
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FAB NC10.14 - HEAVY CHAINBH228Mus musculusMutation(s): 0 
Gene Names: Igh-3
Find proteins for P01867 (Mus musculus)
Explore P01867 
Go to UniProtKB:  P01867
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAS
Query on GAS

Download CCD File 
B, H
N-(P-CYANOPHENYL)-N'-DIPHENYLMETHYL-GUANIDINE-ACETIC ACID
C23 H20 N4 O2
KGHMYJFHUHFOGL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GASKd :  58   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.211 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.9α = 106.7
b = 66.3β = 107.6
c = 75.2γ = 97.3
Software Package:
Software NamePurpose
X-GENdata scaling
X-GENdata reduction
MERLOTphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description