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



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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAINA, C, E, G192Mus musculusMutation(s): 2 
Gene Names: IEK
Find proteins for P04224 (Mus musculus)
Explore P04224 
Go to UniProtKB:  P04224
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
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
Find proteins for P02089 (Mus musculus)
Explore P02089 
Go to UniProtKB:  P02089
Find proteins for P04230 (Mus musculus)
Explore P04230 
Go to UniProtKB:  P04230
NIH Common Fund Data Resources
IMPC  MGI:95901
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N/A
2 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, C, D, E, F, G, H
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: 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

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Entry History 

Deposition Data

Revision History 

  • 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