PDBsum entry 2icw

Immune system

PDB id: 2icw

Contents

Protein chains

179 a.a. *

184 a.a. *

13 a.a. *

213 a.a. *

110 a.a. *

113 a.a. *

Waters ×305

* Residue conservation analysis

PDB id:

2icw

Name:

Immune system

Title:

Crystal structure of a complete ternary complex between tcr, superantigen, and peptide-mhc class ii molecule

Structure:

Hla class ii histocompatibility antigen, dr alpha chain. Chain: a, d. Fragment: residues 28-206. Synonym: mhc class ii antigen dra. Engineered: yes. Hla class ii histocompatibility antigen, drb1-1 beta chain. Chain: b, e. Fragment: residues 30-219. Synonym: mhc class ii antigen drb1 1, Dr-1, dr1.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hla-dra. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: hla-drb1. Synthetic: yes. Other_details: this sequence occurs naturally in influenza virus.

Resolution:

2.41Å R-factor: 0.242 R-free: 0.288

Authors:

L.Wang,Y.Zhao,H.Li

Key ref:

L.Wang et al. (2007). Crystal structure of a complete ternary complex of TCR, superantigen and peptide-MHC. Nat Struct Mol Biol, 14, 169-171. PubMed id: 17220897 DOI: 10.1038/nsmb1193

Date:

13-Sep-06 Release date: 20-Mar-07

Protein chains

P01903  (DRA_HUMAN) -  HLA class II histocompatibility antigen, DR alpha chain from Homo sapiens

Seq: 254 a.a.

Struc: 179 a.a.

Protein chains

P01911  (2B1F_HUMAN) -  HLA class II histocompatibility antigen, DRB1 beta chain from Homo sapiens

Seq: 266 a.a.

Struc: 184 a.a.*

Protein chains

No UniProt id for this chain

Struc: 13 a.a.

Protein chains

Q48898  (Q48898_METAT) -  Superantigen from Metamycoplasma arthritidis

Seq: 238 a.a.

Struc: 213 a.a.

Protein chains

P01738  (TVA1_MOUSE) -  T-cell receptor alpha chain V region PHDS58 from Mus musculus

Seq: 130 a.a.

Struc: 110 a.a.*

Protein chains

A2NTY6  (A2NTY6_MOUSE) -  Beta-chain (Fragment) from Mus musculus

Seq: 144 a.a.

Struc: 113 a.a.*

* PDB and UniProt seqs differ at 22 residue positions (black crosses)

DOI no: 10.1038/nsmb1193

Nat Struct Mol Biol 14:169-171 (2007)

PubMed id: 17220897

Crystal structure of a complete ternary complex of TCR, superantigen and peptide-MHC.

L.Wang, Y.Zhao, Z.Li, Y.Guo, L.L.Jones, D.M.Kranz, W.Mourad, H.Li.

ABSTRACT

'Superantigens' (SAgs) trigger the massive activation of T cells by simultaneous interactions with MHC and TCR receptors, leading to human diseases. Here we present the first crystal structure, at 2.5-A resolution, of a complete ternary complex between a SAg and its two receptors, HLA-DR1/HA and TCR. The most striking finding is that the SAg Mycoplasma arthritidis mitogen, unlike others, has direct contacts not only with TCR Vbeta but with TCR Valpha.

Selected figure(s)

Figure 1.
Figure 1. Crystal structure of scTCR–MAM–HLA-DR1/HA ternary complex. Lime, MAM; blue, DR1 ; cyan, DR1 ; red, HA; purple, TCR V ; green, TCR V . (a) Structure of the scTCR–MAM–HLA-DR1/HA complex. (b) Interaction surfaces of MAM and scTCR T7. Center, surface presentation of the MAM–scTCR structure; left, opened-up view of the MAM-binding surface of scTCR; right, opened-up view of the TCR-binding surface of MAM. Hydrophobic surface patches are colored in cyan. CDR and HV4 loops of TCR are shown as 'worms'. Selected aromatic residues of TCR at the interface are shown as rods. (c) Sequence alignment of the V residues of MAM-reactive (indicated by +) and unreactive (-) TCRs. Conserved or conservatively substituted residues (red boxes) and MAM-contacting residues (red asterisks) are indicated. (d) Sequence alignment of MAM-contacting residues of TCR V s that are most frequently activated by MAM (indicated by +) and TCR V s that are less frequently activated by MAM. Conserved residues indicated as in c; green boxes mark strictly conserved cysteine residues.

Figure 2.
Figure 2. Conformational changes in MAM and TCR upon complex formation. (a) Superposition of the MAM–HLA-DR1/HA complex (green) determined in our earlier study^13 onto its counterpart (red) in the ternary complex. The MAM CTD is not included in superposition. (b) Superposition of the MAM CTD in the previous MAM–HLA-DR1/HA binary complex^13 onto its counterpart (red) in the ternary complex. (c) Superposition of the ligand-free TCR-2C (ref. 2), and TCR-2C in complexes with H-2K^b MHC I with an agonist^14 and a superagonist peptide^15, onto TCR T7 in our ternary complex. Light gray, non-CDR regions; purple, CDRs of V ; green, T7 V ; lime, free 2C; pink, 2C with agonist peptide; cyan, 2C with superagonist peptide.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2007, 14, 169-171) copyright 2007.