1IAK

HISTOCOMPATIBILITY ANTIGEN I-AK

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


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

  • DOI: 10.1016/s1074-7613(00)80536-1
  • Primary Citation of Related Structures:  
    1IAK

  • 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 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.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA. fremont@immunology.wustl.edu



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC CLASS II I-AKA199Mus musculusMutation(s): 0 
Gene Names: H2-Aa
UniProt
Find proteins for P01910 (Mus musculus)
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Go to UniProtKB:  P01910
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UniProt GroupP01910
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MHC CLASS II I-AKB185Mus musculusMutation(s): 0 
Gene Names: H2-Ab1
UniProt
Find proteins for P06343 (Mus musculus)
Explore P06343 
Go to UniProtKB:  P06343
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UniProt GroupP06343
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MHC CLASS II I-AKC [auth P]13Mus musculusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for Q29431 (Ovis aries)
Explore Q29431 
Go to UniProtKB:  Q29431
Entity Groups  
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UniProt GroupQ29431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth B]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.25α = 90
b = 112.25β = 90
c = 99.72γ = 90
Software Package:
Software NamePurpose
HKLdata collection
DENZOdata reduction
SCALAdata scaling
Agrovatadata reduction
X-PLORmodel building
X-PLORrefinement
HKLdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-04-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary