Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.18 kDa 
• Atom Count: 1779 
• Modelled Residue Count: 221 
• Deposited Residue Count: 221 
• Unique protein chains: 2

1DL7

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

• PDB DOI: 10.2210/pdb1DL7/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-12-08 Released: 2000-12-13 
• Deposition Author(s): Schumacher, M., Brown, M.

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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 

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

• PubMed: 10859335 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ANTIBODY M3C65 (LIGHT CHAIN))	A [auth L]	109	Mus musculus	Mutation(s): 0  Gene Names: HYBRIDOMA M3C65
UniProt
Find proteins for P01724 (Mus musculus) Explore P01724  Go to UniProtKB:  P01724

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ANTIBODY M3C65 (HEAVY CHAIN))	B [auth H]	112	Mus musculus	Mutation(s): 0  Gene Names: HYBRIDOMA M3C65
UniProt
Find proteins for P01820 (Mus musculus) Explore P01820  Go to UniProtKB:  P01820

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCH	C [auth L]	P-NITROPHENYL-PHOSPHOCHOLINE C11 H18 N2 O6 P NAIXASFEPQPICN-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding 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 = 130.9	α = 90
b = 35.9	β = 90
c = 50.45	γ = 90

Software Package:

Software Name	Purpose
bioteX	data collection
bioteX	data reduction
EPMR	phasing
TNT	refinement
bioteX	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-12-08 
• Released Date: 2000-12-13 
Deposition Author(s): Schumacher, M., Brown, M.

Revision History  

• 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