1I3R

CRYSTAL STRUCTURE OF A MUTANT IEK CLASS II MHC MOLECULE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.229 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Mutations changing the kinetics of class II MHC peptide exchange.

Wilson, N.Fremont, D.Marrack, P.Kappler, J.

(2001) Immunity 14: 513-522

  • DOI: 10.1016/s1074-7613(01)00140-6
  • Primary Citation of Related Structures:  
    1I3R

  • PubMed Abstract: 
  • IE/DR MHC class II molecules have an extensive H-bonding network under the bound peptide. In IE(k), two alpha chain acidic amino acids in the core of this network were mutated to amides. At low pH, the mutant molecule exchanged peptide much more rapidly than the wild-type ...

    IE/DR MHC class II molecules have an extensive H-bonding network under the bound peptide. In IE(k), two alpha chain acidic amino acids in the core of this network were mutated to amides. At low pH, the mutant molecule exchanged peptide much more rapidly than the wild-type. The crystal structure of the mutant IE(k) revealed the loss of a single buried water molecule and a reorganization of the predicted H-bonding network. We suggest that these mutations enhance the transition of MHC class II to an open conformation at low pH allowing the bound peptide to escape. In wild-type IE(k), the need to protonate these amino acids also may be a bottleneck in the return to a closed conformation after peptide binding.


    Organizational Affiliation

    Howard Hughes Medical Institute, Integrated Department of Immunology, Zuckerman Family/Canyon, Ranch Crystallography Laboratory, National Jewish Medical and Research Center, Denver, CO 80206, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAINA, C, E, G192Mus musculusMutation(s): 2 
Gene Names: IEK
UniProt
Find proteins for P04224 (Mus musculus)
Explore P04224 
Go to UniProtKB:  P04224
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAINB, D, F, H228Mus musculusMutation(s): 0 
Gene Names: IEK
UniProt & NIH Common Fund Data Resources
Find proteins for P02089 (Mus musculus)
Explore P02089 
Go to UniProtKB:  P02089
Find proteins for P04230 (Mus musculus)
Explore P04230 
Go to UniProtKB:  P04230
IMPC:  MGI:95901
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI, J, K, L2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.059α = 90
b = 58.02β = 93.24
c = 143.222γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • 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
  • Version 2.1: 2021-10-27
    Changes: Database references, Structure summary