1IEB

HISTOCOMPATIBILITY ANTIGEN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history. 


Literature

Structures of an MHC class II molecule with covalently bound single peptides.

Fremont, D.H., Hendrickson, W.A., Marrack, P., Kappler, J.

(1996) Science 272: 1001-1004

  • DOI: https://doi.org/10.1126/science.272.5264.1001
  • Primary Citation of Related Structures:  
    1IEA, 1IEB

  • PubMed Abstract: 

    The high-resolution x-ray crystal structures of the murine major histocompatibility complex (MHC) class II molecule, I-E(k), occupied by either of two antigenic peptides were determined. They reveal the structural basis for the I-E(k) peptide binding motif and suggest general principles for additional alleles. A buried cluster of acidic amino acids in the binding groove predicted to be conserved among all murine I-E and human DR MHC class II molecules suggests how pH may influence MHC binding or exchange of peptides. These structures also complement mutational studies on the importance of individual peptide residues to T cell receptor recognition.

    • Organizational Affiliation: 

    Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, 10032, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC CLASS II I-EK
A, C
192Mus musculusMutation(s): 0 
UniProt
Find proteins for P01904 (Mus musculus)
Explore P01904 
Go to UniProtKB:  P01904
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01904
Glycosylation
Glycosylation Sites: 2
Go to GlyGen: P01904-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MHC CLASS II I-EK
B, D
227Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q31164 (Mus musculus)
Explore Q31164 
Go to UniProtKB:  Q31164
IMPC:  MGI:95901
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31164
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.53α = 90
b = 77.53β = 90
c = 319.48γ = 120
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: 1997-06-05
    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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2023-08-09
    Changes: Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Data collection, Structure summary