PDBsum entry 1d9k

Immune system

PDB id: 1d9k

Contents

Protein chains

110 a.a. *

112 a.a. *

183 a.a. *

188 a.a. *

16 a.a. *

Ligands

NAG-NDG ×4

NAG ×2

* Residue conservation analysis

PDB id:

1d9k

Name:

Immune system

Title:

Crystal structure of complex between d10 tcr and pmhc i-ak/ca

Structure:

T-cell receptor d10 (alpha chain). Chain: a, e. Engineered: yes. Mutation: yes. T-cell receptor d10 (beta chain). Chain: b, f. Engineered: yes. Mhc i-ak a chain (alpha chain). Chain: c, g.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Expressed in: cricetulus griseus. Expression_system_taxid: 10029.

Biol. unit:

Tetramer (from PQS)

Resolution:

3.20Å R-factor: 0.247 R-free: 0.293

Authors:

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

Key ref:

E.L.Reinherz et al. (1999). The crystal structure of a T cell receptor in complex with peptide and MHC class II. Science, 286, 1913-1921. PubMed id: 10583947 DOI: 10.1126/science.286.5446.1913

Date:

28-Oct-99 Release date: 15-Dec-99

Protein chains

P01739  (TVA2_MOUSE) -  T-cell receptor alpha chain V region 2B4 from Mus musculus

Seq: 132 a.a.

Struc: 110 a.a.*

Protein chains

P04213  (TVB5_MOUSE) -  T-cell receptor beta chain V region C5 (Fragment) from Mus musculus

Seq: 122 a.a.

Struc: 112 a.a.*

Protein chains

P01910  (HA2K_MOUSE) -  H-2 class II histocompatibility antigen, A-K alpha chain from Mus musculus

Seq: 256 a.a.

Struc: 183 a.a.

Protein chains

P06343  (HB2K_MOUSE) -  H-2 class II histocompatibility antigen, A-K beta chain from Mus musculus

Seq: 263 a.a.

Struc: 188 a.a.*

Protein chains

P02789  (TRFE_CHICK) -  Ovotransferrin from Gallus gallus

Seq: 705 a.a.

Struc: 16 a.a.*

* PDB and UniProt seqs differ at 66 residue positions (black crosses)

DOI no: 10.1126/science.286.5446.1913

Science 286:1913-1921 (1999)

PubMed id: 10583947

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

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

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.

Selected figure(s)

Figure 4.
Fig. 4. The high point "ridge" in pMHCII ligands is created, in part, by the peptide. (A) Hydrogen bond network between the CA peptide and I-A^k. The 10 hydrogen bonds between the CA and I-A^k are shown as magenta dashed lines. These bonds are conserved in known pMHCII structures. The helical regions from I-A^k (colors as in Fig. 3) are shown as a backbone worm diagram with those side chains and main-chain atoms involved in the interactions displayed. The H2 1 helix and H2a and H2b 1 helices are labeled. (B) Stereo view of the molecular surface of I-A^k ( 1 1) together with the CA peptide (red), showing the surface topology of the D10 docking platform on the CA/I-A^k ligand. (C) Stereo view of the molecular surface of H-2Kb ( 1/ 2) together with the dEV8 peptide (red) (6, 7) in the same view as in (B), showing the smaller high point on the left side of the docking platform for the MHC class I-restricted TCR molecule. The peptide is mostly buried and makes little, if any, contribution to the elevated points. Those residues contributing to the high points of the platform are labeled in cyan in (B) and (C).

Figure 6.
Fig. 6. Model of the scD10-SEB-pMHCII interaction complex. (A) Superposition of the V C -SEB complex (in dark blue) and the scD10-CA/I-A^k complex. The V domains from each complex were used for least-square fitting (92 C atoms from residues Val3-Gly94 of V , rmsd = 0.67 Å). The color scheme for the complex of D10-CA/I-A^k is as labeled. (B) The superposition of the SEB/HLA-DR1 complex (in brown) to the already superimposed V C -SEB complex (in dark blue) and scD10 (V V ) module derived from (A). The two SEB superantigen molecules were used for least-square fitting (83 C atoms, rmsd = 0.63 Å). (C) scD10-SEB-CA/I-A^k interaction complex. DR1 in Fig. 6B has been replaced with I-A^k on the basis of structural alignment of residues of the two helices of each MHC molecule (43 C atoms, rmsd = 1.02 Å).

The above figures are reprinted by permission from the AAAs: Science (1999, 286, 1913-1921) copyright 1999.

Figures were selected by an automated process.