2ICW Immune System date Sep 13, 2006
title Crystal Structure Of A Complete Ternary Complex Between Tcr, Superantigen, And Peptide-Mhc Class II Molecule
authors L.Wang, Y.Zhao, H.Li
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain;
Chain: A, D
Fragment: Residues 28-206
Synonym: Mhc Class II Antigen Dra
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dra
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plm1

Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 Beta Chain;
Chain: B, E
Fragment: Residues 30-219
Synonym: Mhc Class II Antigen Drb11, Dr-1, Dr1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Drb1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plm1

Molecule: Haemagglutinin Peptide
Chain: C, F
Fragment: Residues 306-318
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Influenza Virus;

Molecule: Mycoplasma Arthritidis Mitogen
Chain: G, H
Fragment: Residues 26-238
Engineered: Yes

Organism_scientific: Mycoplasma Arthritidis
Organism_taxid: 2111
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1

Molecule: T-Cell Receptor Alpha Chain V
Chain: I, K
Fragment: Residues 21-131
Engineered: Yes
Mutation: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: T-Cell Receptor Beta Chain V
Chain: J, L
Engineered: Yes
Mutation: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 1
R_factor 0.242 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.516 86.822 116.981 110.27 92.32 107.87
method X-Ray Diffractionresolution 2.41 Å
ligand MSE enzyme
Primary referenceCrystal structure of a complete ternary complex of TCR, superantigen and peptide-MHC., Wang L, Zhao Y, Li Z, Guo Y, Jones LL, Kranz DM, Mourad W, Li H, Nat Struct Mol Biol. 2007 Feb;14(2):169-71. Epub 2007 Jan 14. PMID:17220897
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (279 Kb) [Save to disk]
  • Biological Unit Coordinates (2icw.pdb1.gz) 139 Kb
  • Biological Unit Coordinates (2icw.pdb2.gz) 139 Kb
  • LPC: Ligand-Protein Contacts for 2ICW
  • CSU: Contacts of Structural Units for 2ICW
  • Likely Quarternary Molecular Structure file(s) for 2ICW
  • Structure Factors (663 Kb)
  • Retrieve 2ICW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ICW from S2C, [Save to disk]
  • Re-refined 2icw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ICW 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 2ICW
  • 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 2ICW, from MSDmotif at EBI
  • Fold representative 2icw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2icw_I] [2icw_D] [2icw_B] [2icw] [2icw_C] [2icw_E] [2icw_K] [2icw_G] [2icw_J] [2icw_F] [2icw_H] [2icw_L] [2icw_A]
  • SWISS-PROT database: [P04229] [P01903] [Q48898] [P01738]
  • Domain organization of [2B11_HUMAN] [DRA_HUMAN] [Q48898_MYCAT] [TVA1_MOUSE] by SWISSPFAM
  • Domains found in 2ICW: [IGc1] [IGv] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 2ICW
  • Community annotation for 2ICW 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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