1D9K

CRYSTAL STRUCTURE OF COMPLEX BETWEEN D10 TCR AND PMHC I-AK/CA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of a T cell receptor in complex with peptide and MHC class II.

Reinherz, E.L.Tan, K.Tang, L.Kern, P.Liu, J.Xiong, Y.Hussey, R.E.Smolyar, A.Hare, B.Zhang, R.Joachimiak, A.Chang, H.C.Wagner, G.Wang, J.

(1999) Science 286: 1913-1921


  • PubMed Abstract: 
  • The crystal structure of a complex involving the D10 T cell receptor (TCR), 16-residue foreign peptide antigen, and the I-Ak self major histocompatibility complex (MHC) class II molecule is reported at 3.2 angstrom resolution. The D10 TCR is oriented ...

    The crystal structure of a complex involving the D10 T cell receptor (TCR), 16-residue foreign peptide antigen, and the I-Ak self major histocompatibility complex (MHC) class II molecule is reported at 3.2 angstrom resolution. The D10 TCR is oriented in an orthogonal mode relative to its peptide-MHC (pMHC) ligand, necessitated by the amino-terminal extension of peptide residues projecting from the MHC class II antigen-binding groove as part of a mini beta sheet. Consequently, the disposition of D10 complementarity-determining region loops is altered relative to that of most pMHCI-specific TCRs; the latter TCRs assume a diagonal orientation, although with substantial variability. Peptide recognition, which involves P-1 to P8 residues, is dominated by the Valpha domain, which also binds to the class II MHC beta1 helix. That docking is limited to one segment of MHC-bound peptide offers an explanation for epitope recognition and altered peptide ligand effects, suggests a structural basis for alloreactivity, and illustrates how bacterial superantigens can span the TCR-pMHCII surface.


    Organizational Affiliation

    Laboratory of Immunobiology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-CELL RECEPTOR D10 (ALPHA CHAIN)
A, E
110Mus musculusMutation(s): 1 
Find proteins for P01739 (Mus musculus)
Go to UniProtKB:  P01739
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
T-CELL RECEPTOR D10 (BETA CHAIN)
B, F
112Mus musculusMutation(s): 0 
Find proteins for P04213 (Mus musculus)
Go to UniProtKB:  P04213
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MHC I-AK A CHAIN (ALPHA CHAIN)
C, G
183Mus musculusMutation(s): 0 
Gene Names: H2-Aa
Find proteins for P01910 (Mus musculus)
Go to UniProtKB:  P01910
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MHC I-AK B CHAIN (BETA CHAIN)
D, H
188Mus musculusMutation(s): 0 
Gene Names: H2-Ab1
Find proteins for P06343 (Mus musculus)
Go to UniProtKB:  P06343
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
CONALBUMIN PEPTIDE
P, Q
16Gallus gallusMutation(s): 0 
Find proteins for P02789 (Gallus gallus)
Go to UniProtKB:  P02789
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.247 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 97.600α = 90.00
b = 345.300β = 90.00
c = 97.700γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-02-01
    Type: Structure summary