5D7I Immune System date Aug 14, 2015
title Structure Of Human Mr1-Ac-6-Fp In Complex With Human Mait M3
authors A.N.Keller, R.E.Woolley, J.Rossjohn
compound source
Molecule: Major Histocompatibility Complex Class I-Related Protein;
Chain: A, C
Fragment: Extracellular Domain Residues 23-292
Synonym: Mhc Class I-Related Gene Protein,Class I Histocomp Antigen-Like Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mr1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30

Molecule: Beta-2-Microglobulin
Chain: B, D
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: B2m, Cdabp0092, Hdcma22p
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30

Molecule: M33.64 Tcr Alpha Chain
Chain: G, E
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Travtrav
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30

Molecule: M33.64 Tcr Beta Chain
Chain: H, F
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Trbvtrbc
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30
symmetry Space Group: C 1 2 1
R_factor 0.178 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
214.300 69.660 141.190 90.00 103.99 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 30W, GOL, PRO enzyme
Gene
Ontology
ChainFunctionProcessComponent
D, B
  • cellular response to iron io...

  • Primary referenceDiversity of T Cells Restricted by the MHC Class I-Related Molecule MR1 Facilitates Differential Antigen Recognition., Gherardin NA, Keller AN, Woolley RE, Le Nours J, Ritchie DS, Neeson PJ, Birkinshaw RW, Eckle SB, Waddington JN, Liu L, Fairlie DP, Uldrich AP, Pellicci DG, McCluskey J, Godfrey DI, Rossjohn J, Immunity. 2016 Jan 19;44(1):32-45. doi: 10.1016/j.immuni.2015.12.005. Epub 2016, Jan 12. PMID:26795251
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (567 Kb) [Save to disk]
  • Biological Unit Coordinates (5d7i.pdb1.gz) 279 Kb
  • Biological Unit Coordinates (5d7i.pdb2.gz) 281 Kb
  • LPC: Ligand-Protein Contacts for 5D7I
  • CSU: Contacts of Structural Units for 5D7I
  • Structure Factors (7272 Kb)
  • Retrieve 5D7I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D7I from S2C, [Save to disk]
  • Re-refined 5d7i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5D7I 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 5D7I
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d7i_D] [5d7i_F] [5d7i_H] [5d7i_C] [5d7i_A] [5d7i_E] [5d7i_G] [5d7i_B] [5d7i]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5D7I: [IG_like] [IGc1] [IGv ] by SMART
  • Other resources with information on 5D7I
  • Community annotation for 5D7I at PDBWiki (http://pdbwiki.org)

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