1MHC

MODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED AT 2.3 ANGSTROMS RESOLUTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Nonclassical binding of formylated peptide in crystal structure of the MHC class Ib molecule H2-M3

Wang, C.R., Castano, A.R., Peterson, P.A., Slaughter, C., Lindahl, K.F., Deisenhofer, J.

(1995) Cell 82: 655-664


  • PubMed Abstract: 

    • H2-M3 is a class Ib MHC molecule of the mouse with a 10(4)-fold preference for binding N-formylated peptides. To elucidate the basis of this unusual specificity, we expressed and crystallized a soluble form of M3 with a formylated nonamer peptide, fM ...

    H2-M3 is a class Ib MHC molecule of the mouse with a 10(4)-fold preference for binding N-formylated peptides. To elucidate the basis of this unusual specificity, we expressed and crystallized a soluble form of M3 with a formylated nonamer peptide, fMYFINILTL, and determined the structure by X-ray crystallography. M3, refined at 2.1 A resolution, resembles class la MHC molecules in its overall structure, but differs in the peptide-binding groove. The A pocket, which usually accommodates the free N-terminus of a bound peptide, is closed, and the peptide is shifted one residue, such that the P1 side chain is lodged in the B pocket. The formyl group is coordinated by His-9 and a bound water on the floor of the groove.

    Related Citations: 
    • H-2M3 Encodes the Mhc Class I Molecule Presenting the Maternally Transmitted Antigen of the Mouse
      Wang, C.-R.,Loveland, B.E.,Fischer Lindahl, K.
      (1991) Cell 66: 335

    Organizational Affiliation: 

    Department of Biochemistry, University of Texas Southwestern Medical Center Dallas 75235-9050, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS I ANTIGEN H2-M3
A, D
282Mus musculusMutation(s): 0 
Gene Names: H2-M3 (H-2M3)
Find proteins for Q31093 (Mus musculus)
Go to UniProtKB:  Q31093
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS I ANTIGEN H2-M3
B, E
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NONAPEPTIDE FROM RAT NADH DEHYDROGENASE
C, F
9Rattus norvegicusMutation(s): 0 
Gene Names: Mtnd1 (mt-Nd1, Nd1)
EC: 7.1.1.2
Find proteins for P03889 (Rattus norvegicus)
Go to UniProtKB:  P03889
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download SDF File 
Download CCD File 
D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
C, F
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.190 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 65.250α = 102.71
b = 66.100β = 96.28
c = 55.170γ = 110.19
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-01-29
    Type: Initial release
  • Version 1.1: 2008-03-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance