3T0E Immune System date Jul 20, 2011
title Crystal Structure Of A Complete Ternary Complex Of T Cell Re Peptide-Mhc And Cd4
authors Y.Yin, R.A.Mariuzza
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: A
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
Fragment: Unp Residues 30-221
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
Chain: C
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
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 Chain
Chain: D
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
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 Surface Glycoprotein Cd4
Chain: E
Fragment: Unp Residues 26-398
Synonym: T-Cell Surface Antigen T4leu-3
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd4
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacgp67b
symmetry Space Group: P 43 21 2
R_factor 0.238 R_Free 0.305
crystal
cell
length a length b length c angle alpha angle beta angle gamma
146.151 146.151 231.436 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.00 Å
Primary referenceCrystal structure of a complete ternary complex of T-cell receptor, peptide-MHC, and CD4., Yin Y, Wang XX, Mariuzza RA, Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5405-10. Epub 2012 Mar 19. PMID:22431638
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (416 Kb) [Save to disk]
  • Biological Unit Coordinates (3t0e.pdb1.gz) 406 Kb
  • CSU: Contacts of Structural Units for 3T0E
  • Structure Factors (176 Kb)
  • Retrieve 3T0E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3T0E from S2C, [Save to disk]
  • Re-refined 3t0e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3T0E 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 3T0E
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3T0E, from MSDmotif at EBI
  • Fold representative 3t0e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3t0e] [3t0e_A] [3t0e_D] [3t0e_B] [3t0e_E] [3t0e_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3T0E: [IG] [IGc1] [IGv] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 3T0E with the sequences similar proteins can be viewed for 3T0E'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 3T0E
  • Community annotation for 3T0E at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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