1DL7

THE STRUCTURAL BASIS OF REPERTOIRE SHIFT IN AN IMMUNE RESPONSE TO PHOSPHOCHOLINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The structural basis of repertoire shift in an immune response to phosphocholine.

Brown, M.Schumacher, M.A.Wiens, G.D.Brennan, R.G.Rittenberg, M.B.

(2000) J Exp Med 191: 2101-2112

  • DOI: 10.1084/jem.191.12.2101
  • Primary Citation of Related Structures:  
    1DL7

  • PubMed Abstract: 
  • The immune response to phosphocholine (PC)-protein is characterized by a shift in antibody repertoire as the response progresses. This change in expressed gene combinations is accompanied by a shift in fine specificity toward the carrier, resulting in high affinity to PC-protein ...

    The immune response to phosphocholine (PC)-protein is characterized by a shift in antibody repertoire as the response progresses. This change in expressed gene combinations is accompanied by a shift in fine specificity toward the carrier, resulting in high affinity to PC-protein. The somatically mutated memory hybridoma, M3C65, possesses high affinity for PC-protein and the phenyl-hapten analogue, p-nitrophenyl phosphocholine (NPPC). Affinity measurements using related PC-phenyl analogues, including peptides of varying lengths, demonstrate that carrier determinants contribute to binding affinity and that somatic mutations alter this recognition. The crystal structure of an M3C65-NPPC complex at 2.35-A resolution allows evaluation of the three light chain mutations that confer high-affinity binding to NPPC. Only one of the mutations involves a contact residue, whereas the other two have indirect effects on the shape of the combining site. Comparison of the M3C65 structure to that of T15, an antibody dominating the primary response, provides clear structural evidence for the role of carrier determinants in promoting repertoire shift. These two antibodies express unrelated variable region heavy and light chain genes and represent a classic example of the effect of repertoire shift on maturation of the immune response.


    Organizational Affiliation

    Department of Molecular Microbiology and Immunology, Portland, Oregon 97201-3098, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ANTIBODY M3C65 (LIGHT CHAIN))A [auth L]109Mus musculusMutation(s): 0 
Gene Names: HYBRIDOMA M3C65
UniProt
Find proteins for P01724 (Mus musculus)
Explore P01724 
Go to UniProtKB:  P01724
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01724
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ANTIBODY M3C65 (HEAVY CHAIN))B [auth H]112Mus musculusMutation(s): 0 
Gene Names: HYBRIDOMA M3C65
UniProt
Find proteins for P01820 (Mus musculus)
Explore P01820 
Go to UniProtKB:  P01820
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01820
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCH
Query on NCH

Download Ideal Coordinates CCD File 
C [auth L]P-NITROPHENYL-PHOSPHOCHOLINE
C11 H18 N2 O6 P
NAIXASFEPQPICN-UHFFFAOYSA-O
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NCH PDBBind:  1DL7 Kd: 320 (nM) from 1 assay(s)
Binding MOAD:  1DL7 Kd: 320 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.9α = 90
b = 35.9β = 90
c = 50.45γ = 90
Software Package:
Software NamePurpose
bioteXdata collection
bioteXdata reduction
EPMRphasing
TNTrefinement
bioteXdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-13
    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: 2013-10-02
    Changes: Source and taxonomy
  • Version 1.4: 2017-10-04
    Changes: Refinement description