PDBsum entry 2icw

Go to PDB code: 
protein Protein-protein interface(s) links
Immune system PDB id
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:
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.
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
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
13-Sep-06     Release date:   20-Mar-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P01903  (DRA_HUMAN) -  HLA class II histocompatibility antigen, DR alpha chain
254 a.a.
179 a.a.
Protein chains
Pfam   ArchSchema ?
P04229  (2B11_HUMAN) -  HLA class II histocompatibility antigen, DRB1-1 beta chain
266 a.a.
184 a.a.
Protein chains
No UniProt id for this chain
Struc: 13 a.a.
Protein chains
Pfam   ArchSchema ?
Q48898  (Q48898_MYCAT) -  Superantigen
238 a.a.
213 a.a.
Protein chains
Pfam   ArchSchema ?
P01738  (TVA1_MOUSE) -  T-cell receptor alpha chain V region PHDS58
130 a.a.
110 a.a.*
Protein chains
Pfam   ArchSchema ?
A2NTY6  (A2NTY6_MOUSE) -  Beta-chain (Fragment)
144 a.a.
113 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     immune response   2 terms 


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.
'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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21364947 J.M.Khan, and S.Ranganathan (2011).
Understanding TR Binding to pMHC Complexes: How Does a TR Scan Many pMHC Complexes yet Preferentially Bind to One.
  PLoS One, 6, e17194.  
20040916 E.Lemichez, M.Lecuit, X.Nassif, and S.Bourdoulous (2010).
Breaking the wall: targeting of the endothelium by pathogenic bacteria.
  Nat Rev Microbiol, 8, 93.  
21081917 M.Saline, K.E.Rödström, G.Fischer, V.Y.Orekhov, B.G.Karlsson, and K.Lindkvist-Petersson (2010).
The structure of superantigen complexed with TCR and MHC reveals novel insights into superantigenic T cell activation.
  Nat Commun, 1, 119.
PDB codes: 2xn9 2xna
18962897 S.A.Richman, D.H.Aggen, M.L.Dossett, D.L.Donermeyer, P.M.Allen, P.D.Greenberg, and D.M.Kranz (2009).
Structural features of T cell receptor variable regions that enhance domain stability and enable expression as single-chain ValphaVbeta fragments.
  Mol Immunol, 46, 902-916.  
18674935 J.P.Cannon, R.N.Haire, A.T.Magis, D.D.Eason, K.N.Winfrey, J.A.Hernandez Prada, K.M.Bailey, J.Jakoncic, G.W.Litman, and D.A.Ostrov (2008).
A bony fish immunological receptor of the NITR multigene family mediates allogeneic recognition.
  Immunity, 29, 228-237.
PDB codes: 2qhl 2qjd 2qqq 2qte 3b5t 3bdb
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.