Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 46.95 kDa 
• Atom Count: 3597 
• Residue Count: 379 
• Unique protein chains: 3

1K2D

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

• DOI: 10.2210/pdb1K2D/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2001-09-26 Released: 2003-03-04 
• Deposition Author(s): He, X.L., Radu, C., Ward, E.S., Garcia, K.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.276 
• R-Value Work: 0.248 
• R-Value Observed: 0.249 

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: 12150894 
• DOI: 10.1016/s1074-7613(02)00340-0
• Primary Citation of Related Structures:  
  1K2D


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class II histocompatibility antigen, A-U alpha chain	A	189	Mus musculus	Mutation(s): 0  Gene Names: H2-Aa
Find proteins for P14438 (Mus musculus) Explore P14438  Go to UniProtKB:  P14438

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class II histocompatibility antigen, A-U beta chain	B	189	Mus musculus	Mutation(s): 0
Find proteins for P06344 (Mus musculus) Explore P06344  Go to UniProtKB:  P06344

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Myelin Basic Protein peptide with 8 residue linker peptide	P	23	N/A	Mutation(s): 0
Find proteins for P02686 (Homo sapiens) Explore P02686  Go to UniProtKB:  P02686
NIH Common Fund Data Resources
PHAROS  P02686 GTEx  ENSG00000197971

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.276 
• R-Value Work: 0.248 
• R-Value Observed: 0.249 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.15	α = 90
b = 110.59	β = 90
c = 94.84	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-09-26 
• Released Date: 2003-03-04 
Deposition Author(s): He, X.L., Radu, C., Ward, E.S., Garcia, K.C.

Revision History 

• Version 1.0: 2003-03-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary