Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer -A2 

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

Macromolecule Content

• Total Structure Weight: 46794.20 
• Atom Count: 3171 
• Residue Count: 397 
• Unique protein chains: 3

1IAK

HISTOCOMPATIBILITY ANTIGEN I-AK

• DOI: 10.2210/pdb1IAK/pdb

• Classification: HISTOCOMPATIBILITY ANTIGEN I-AK
• Organism(s): Ovis aries, Mus musculus
• Expression System: CHO CELLS AS GPI-LINKED PROTEIN


• Deposited: 1997-11-18 Released: 1998-04-15 
• Deposition Author(s): Fremont, D.H., Unanue, E.R., Hendrickson, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.263 
• R-Value Work: 0.214 

Literature

Crystal structure of I-Ak in complex with a dominant epitope of lysozyme.

Fremont, D.H., Monnaie, D., Nelson, C.A., Hendrickson, W.A., Unanue, E.R.

(1998) Immunity 8: 305-317

• PubMed: 9529148 


• PubMed Abstract: 
  

We have determined the structure of murine MHC class II I-Ak in complex with a naturally processed peptide from hen egg lysozyme (HEL residues 50-62) at 1.9 A resolution. These results provide a structural basis for the I-Ak peptide-binding motif. Binding is established by the deep burial of five anchor side chains into specific pockets of the I-Ak binding groove, with a zen-like fit of an aspartic acid in the P1 pocket. We also show that in the I-Ak alpha chain, a bulge occurs in the first strand of the peptide-binding platform, an insertion probably common to all I-A and HLA-DQ alleles. The I-Ak beta chain has a deletion in the helical region adjacent to the P7 pocket and an insertion in the helical region neighboring the P1 pocket. As a result of these structural features, the extended HEL peptide dips low into the center of the I-Ak groove and reaches toward solvent at its C-terminal end.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
MHC CLASS II I-AK	A	199	Mus musculus	Mutation(s): 0  Gene Names: H2-Aa
Find proteins for P01910 (Mus musculus) Go to UniProtKB:  P01910

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
MHC CLASS II I-AK	B	185	Mus musculus	Mutation(s): 0  Gene Names: H2-Ab1
Find proteins for P06343 (Mus musculus) Go to UniProtKB:  P06343

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
MHC CLASS II I-AK	P	13	Ovis aries	Mutation(s): 0
Find proteins for Q29431 (Ovis aries) Go to UniProtKB:  Q29431

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.263 
• R-Value Work: 0.214 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 112.250	α = 90.00
b = 112.250	β = 90.00
c = 99.720	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement
AGROVATA	data reduction
X-PLOR	phasing
HKL	data reduction
SCALA	data scaling
X-PLOR	model building
HKL	data collection
DENZO	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-11-18 
• Released Date: 1998-04-15 
• Deposition Author(s): Fremont, D.H., Unanue, E.R., Hendrickson, W.A.

Revision History 

• Version 1.0: 1998-04-15
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2011-11-16
  Type: Atomic model