1D9K

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.293 (Depositor) 
  • R-Value Work: 
    0.247 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.070 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 2.3 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

  • DOI: https://doi.org/10.1126/science.286.5446.1913
  • Primary Citation of Related Structures:  
    1D9K

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-CELL RECEPTOR D10 (ALPHA CHAIN)A,
F [auth E]
110Mus musculusMutation(s): 1 
UniProt
Find proteins for P01739 (Mus musculus)
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UniProt GroupP01739
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-CELL RECEPTOR D10 (BETA CHAIN)B,
G [auth F]
112Mus musculusMutation(s): 0 
UniProt
Find proteins for P04213 (Mus musculus)
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UniProt GroupP04213
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MHC I-AK A CHAIN (ALPHA CHAIN)C,
H [auth G]
183Mus musculusMutation(s): 0 
UniProt
Find proteins for P01910 (Mus musculus)
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UniProt GroupP01910
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P01910-1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MHC I-AK B CHAIN (BETA CHAIN)D,
I [auth H]
188Mus musculusMutation(s): 0 
UniProt
Find proteins for P06343 (Mus musculus)
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UniProt GroupP06343
Glycosylation
Glycosylation Sites: 1
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  • Reference Sequence

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CONALBUMIN PEPTIDEE [auth P],
J [auth Q]
16Mus musculusMutation(s): 0 
UniProt
Find proteins for P02789 (Gallus gallus)
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Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth I],
L [auth J],
M [auth K],
N [auth L]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG
GlyCosmos:  G07375KG
GlyGen:  G07375KG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.293 (Depositor) 
  • R-Value Work:  0.247 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.070 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.6α = 90
b = 345.3β = 90
c = 97.7γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-02-01
    Changes: Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-11-03
    Changes: Database references, Derived calculations, Structure summary
  • Version 2.2: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-11-20
    Changes: Structure summary