2XN9 Immune System date Jul 31, 2010
title Crystal Structure Of The Ternary Complex Between Human T Cel Receptor, Staphylococcal Enterotoxin H And Human Major Histocompatibility Complex Class II
authors M.Saline, K.E.J.Rodstrom, G.Fischer, V.Y.Orekhov, B.G.Karlsson, K.Lindkvist-Petersson
compound source
Molecule: T Cell Receptor Alpha Chain C Region
Chain: A
Fragment: Extracellular Domain, Residues 1-95
Engineered: Yes
Mutation: Yes
Other_details: Variable Domain Trav27 Fused To Constant Dom
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: T Lymphocyte
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pgmt7

Molecule: T Cell Receptor Beta-1 Chain C Region
Chain: B
Fragment: Extracellular Domain, Residues 1-130
Engineered: Yes
Mutation: Yes
Other_details: Variable Domain Trbv19 Fused To Constant Dom

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: T Lymphocyte
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pgmt7

Molecule: Enterotoxin H
Chain: C
Synonym: Seh, Staphylococcal Enterotoxin H
Engineered: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Expression_system: Escherichia Coli
Expression_system_taxid: 83333
Expression_system_strain: K-12
Expression_system_variant: Ul635

Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: D
Fragment: Extracellular Domain, Residues 26-207
Synonym: Major Histocompatibility Complex Class II Alpha, M II Antigen Dra Chain;
Engineered: Yes
Other_details: Chain Dr 0101

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Antigen Presenting Cell
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plys
Expression_system_plasmid: Plm1

Molecule: Major Histocompatibility Complex Class II Beta Ch
Chain: E
Fragment: Extracellular Domain, Residues 30-219
Synonym: Mhc Class II Antigen Drb1.1, Dr-1, Dr1
Engineered: Yes
Other_details: Chain Drb1 0101

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Antigen Presenting Cell
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Plm1

Molecule: Hemagglutinin
Chain: F
Fragment: Residues 59-71
Synonym: Influenza Hemagglutinin Peptide

Synthetic: Yes
Organism_scientific: Influenza A Virus
Organism_taxid: 11320
symmetry Space Group: C 1 2 1
R_factor 0.22150 R_Free 0.27236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
191.180 48.890 166.720 90.00 113.55 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand GOL, NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
C


D


E


Primary referenceThe structure of superantigen complexed with TCR and MHC reveals novel insights into superantigenic T cell activation., Saline M, Rodstrom KE, Fischer G, Orekhov VY, Karlsson BG, Lindkvist-Petersson K, Nat Commun. 2010 Nov 16;1:119. PMID:21081917
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (186 Kb) [Save to disk]
  • Biological Unit Coordinates (2xn9.pdb1.gz) 177 Kb
  • LPC: Ligand-Protein Contacts for 2XN9
  • CSU: Contacts of Structural Units for 2XN9
  • Structure Factors (3237 Kb)
  • Retrieve 2XN9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XN9 from S2C, [Save to disk]
  • Re-refined 2xn9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XN9 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2XN9
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2XN9, from MSDmotif at EBI
  • Fold representative 2xn9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xn9] [2xn9_E] [2xn9_A] [2xn9_D] [2xn9_B] [2xn9_C] [2xn9_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2XN9: [IG] [IGc1] [IGv] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 2XN9 with the sequences similar proteins can be viewed for 2XN9's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2XN9
  • Community annotation for 2XN9 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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