3O6F Immune System date Jul 29, 2010
title Crystal Structure Of A Human Autoimmune Tcr Ms2-3c8 Bound To II Self-Ligand Mbphla-Dr4
authors Y.Yin, Y.Li, R.Martin, R.A.Mariuzza
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: A, E
Fragment: Unp Residues 26-207
Synonym: Mhc Class II Antigen Dra
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dra, Hla-Dra1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plm1

Molecule: Hla Class II Histocompatibility Antigen, Drb1-4 B
Chain: B, F
Fragment: Unp Residues 30-220
Synonym: Mhc Class II Antigen Drb14, Dr-4, Dr4
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Drb1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-26b(+)

Molecule: T-Cell Receptor Alpha Chain C Region
Chain: C, G
Fragment: Unp Residues 1-92
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Trac, Tcra
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-26b(+)

Molecule: T-Cell Receptor Beta-1 Chain C Region
Chain: D, H
Fragment: Unp Residues 1-130
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Trbc1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-26b(+)
symmetry Space Group: P 21 21 2
R_factor 0.239 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.480 218.403 98.412 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
Primary referenceStructure of a TCR with high affinity for self-antigen reveals basis for escape from negative selection., Yin Y, Li Y, Kerzic MC, Martin R, Mariuzza RA, EMBO J. 2011 Feb 4. PMID:21297580
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (269 Kb) [Save to disk]
  • Biological Unit Coordinates (3o6f.pdb1.gz) 133 Kb
  • Biological Unit Coordinates (3o6f.pdb2.gz) 136 Kb
  • CSU: Contacts of Structural Units for 3O6F
  • Structure Factors (447 Kb)
  • Retrieve 3O6F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3O6F from S2C, [Save to disk]
  • Re-refined 3o6f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3O6F 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 3O6F
  • 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 3O6F, from MSDmotif at EBI
  • Fold representative 3o6f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3o6f_B] [3o6f_E] [3o6f_G] [3o6f_F] [3o6f] [3o6f_H] [3o6f_D] [3o6f_A] [3o6f_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3O6F: [IG] [IGc1] [IGv] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 3O6F
  • Community annotation for 3O6F at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science