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: 2.10 Å
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

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This is version 1.3 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

  • DOI: 10.1016/0092-8674(95)90037-3
  • Primary Citation of Related Structures:  
    1MHC

  • 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, fMYFINILTL, and determined the structure by X-ray crystallography ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC CLASS I ANTIGEN H2-M3A, D282Mus musculusMutation(s): 0 
Gene Names: H2-M3 B2MH2-M3H-2M3
UniProt
Find proteins for Q31093 (Mus musculus)
Explore Q31093 
Go to UniProtKB:  Q31093
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MHC CLASS I ANTIGEN H2-M3B, E99Mus musculusMutation(s): 0 
Gene Names: H2-M3 B2MB2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NONAPEPTIDE FROM RAT NADH DEHYDROGENASEC, F9Rattus rattusMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for P03889 (Rattus norvegicus)
Explore P03889 
Go to UniProtKB:  P03889
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
G [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
C, FL-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.25α = 102.71
b = 66.1β = 96.28
c = 55.17γ = 110.19
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-01-29
    Type: Initial release
  • Version 1.1: 2008-03-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary