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
Gene
Ontology
ChainFunctionProcessComponent
A, E


F, B


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
  • Alignments of the sequence of 3O6F with the sequences similar proteins can be viewed for 3O6F'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 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.

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