1I3R

CRYSTAL STRUCTURE OF A MUTANT IEK CLASS II MHC MOLECULE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.3 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


  • 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 rapi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
A, C, E, G
192Mus musculusMutation(s): 2 
Find proteins for P04224 (Mus musculus)
Go to UniProtKB:  P04224
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
B, D, F, H
228Mus musculusMutation(s): 0 
Gene Names: Hbb-b2, H2-Eb1
Find proteins for P02089 (Mus musculus)
Go to UniProtKB:  P02089
Find proteins for P04230 (Mus musculus)
Go to UniProtKB:  P04230
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
D
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, E, F, G, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 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 = 90.00
b = 58.020β = 93.24
c = 143.222γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
AMoREphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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