1LDP

CRYSTAL STRUCTURE OF MURINE MHC CLASS I H-2LD WITH A MIXTURE OF BOUND PEPTIDES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.371 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of 2C TCR allorecognition of H-2Ld peptide complexes.

Speir, J.A.Garcia, K.C.Brunmark, A.Degano, M.Peterson, P.A.Teyton, L.Wilson, I.A.

(1998) Immunity 8: 553-562


  • PubMed Abstract: 
  • MHC class I H-2Ld complexed with peptide QL9 (or p2Ca) is a high-affinity alloantigen for the 2C TCR. We used the crystal structure of H-2Ld with a mixture of bound peptides at 3.1 A to construct a model of the allogeneic 2C-Ld/QL9 complex for compar ...

    MHC class I H-2Ld complexed with peptide QL9 (or p2Ca) is a high-affinity alloantigen for the 2C TCR. We used the crystal structure of H-2Ld with a mixture of bound peptides at 3.1 A to construct a model of the allogeneic 2C-Ld/QL9 complex for comparison with the syngeneic 2C-Kb/dEV8 structure. A prominent ridge on the floor of the Ld peptide-binding groove, not present in Kb, creates a C-terminal bulge in Ld peptides that greatly increases interactions with the 2C beta-chain. Furthermore, weak electrostatic complementarity between Asp77 on the alpha1 helix of Kb and 2C is enhanced in the allogeneic complex by closer proximity of QL9 peptide residue AspP8 to the 2C HV4 loop.


    Related Citations: 
    • Structural Basis of Plasticity in T Cell Receptor Recognition of a Self Peptide-Mhc Antigen
      Garcia, K.C.,Degano, M.,Pease, L.R.,Huang, M.,Peterson, P.A.,Teyton, L.,Wilson, I.A.
      (1998) Science 279: 1166


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS I H-2LD
H
272Mus musculusMutation(s): 0 
Gene Names: H2-L
Find proteins for P01897 (Mus musculus)
Go to UniProtKB:  P01897
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS I H-2LD
L
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE
P
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE
Q
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
H
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.371 
  • R-Value Work: 0.221 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.400α = 90.00
b = 48.980β = 97.95
c = 84.060γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
SCALEPACKdata scaling
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance