1K2D

Crystal structure of the autoimmune MHC class II I-Au complexed with myelin basic protein 1-11 at 2.2A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural snapshot of aberrant antigen presentation linked to autoimmunity: the immunodominant epitope of MBP complexed with I-Au

He, X.L.Radu, C.Sidney, J.Sette, A.Ward, E.S.Garcia, K.C.

(2002) IMMUNITY 17: 83-94


  • PubMed Abstract: 
  • Murine experimental allergic encephalomyelitis (EAE) is a useful model for the demyelinating, autoimmune disease multiple sclerosis. In the EAE system, the immunodominant N-terminal epitope of myelin basic protein (MBP) is an unusually short, weakly ...

    Murine experimental allergic encephalomyelitis (EAE) is a useful model for the demyelinating, autoimmune disease multiple sclerosis. In the EAE system, the immunodominant N-terminal epitope of myelin basic protein (MBP) is an unusually short, weakly binding peptide antigen which elicits highly biased TCR chain usage. In the 2.2 A crystal structure of I-A(u)/MBP1-11 complex, only MBP residues 1-7 are bound toward one end of the peptide binding cleft. The fourth residue of MBP1-11 is located in an incompatible p6 pocket of I-A(u), thus explaining the short half-life of I-A(u) complexed with Ac1-11. MBP peptides extended at the C terminus of Ac1-11 result in dramatic affinity increases, likely attributed to register shifting to a higher affinity cryptic epitope, which could potentially mask the presentation of the immunodominant MBP1-11 peptide during thymic education.


    Organizational Affiliation

    Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class II histocompatibility antigen, A-U alpha chain
A
189Mus musculusGene Names: H2-Aa
Find proteins for P14438 (Mus musculus)
Go to UniProtKB:  P14438
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
H-2 class II histocompatibility antigen, A-U beta chain
B
189Mus musculusN/A
Find proteins for P06344 (Mus musculus)
Go to UniProtKB:  P06344
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Myelin Basic Protein peptide with 8 residue linker peptide
P
23Homo sapiensGene Names: MBP
Find proteins for P02686 (Homo sapiens)
Go to Gene View: MBP
Go to UniProtKB:  P02686
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.248 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 99.150α = 90.00
b = 110.590β = 90.00
c = 94.840γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
MOSFLMdata reduction
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance