3O8X Immune System date Aug 03, 2010
title Recognition Of Glycolipid Antigen By Inkt Cell Tcr
authors D.M.Zajonc, Y.Li
compound source
Molecule: Antigen-Presenting Glycoprotein Cd1d1
Chain: A
Synonym: Cd_antigen
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Cd1.1, Cd1d, Cd1d1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_vector_type: Baculovirus Transfer Vector
Expression_system_vector: Pbacp10ph

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

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: B2m, Beta-2-Microglobulin, Mcg_11606, Rp23-34e24.5-00
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_vector_type: Baculovirus Transfer Vector
Expression_system_vector: Pbacp10ph

Molecule: Valpha14 Chimera (Mouse Variable Domain, Human T- Receptor Alpha Chain C Region Constant Domain);
Chain: C
Engineered: Yes

Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: Mouse, Human
Organism_taxid: 10090,9606
Gene: Trac, Tcra
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21de3
Expression_system_plasmid: Pet22b

Molecule: Vbeta8.2 Chimera (Mouse Variable Domain, Human T- Receptor Beta-2 Chain C Region Constant Domain);
Chain: D
Engineered: Yes

Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: Mouse, Human
Organism_taxid: 10090,9606
Gene: Trbc2, Tcrbc2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21de3
Expression_system_plasmid: Pet30a
symmetry Space Group: C 2 2 21
R_factor 0.195 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
79.000 191.200 151.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.74 Å
ligand FUC, GSL, NAG enzyme
Gene MCG
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceThe V{alpha}14 invariant natural killer T cell TCR forces microbial glycolipids and CD1d into a conserved binding mode., Li Y, Girardi E, Wang J, Yu ED, Painter GF, Kronenberg M, Zajonc DM, J Exp Med. 2010 Oct 4. PMID:20921281
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (286 Kb) [Save to disk]
  • Biological Unit Coordinates (3o8x.pdb1.gz) 279 Kb
  • LPC: Ligand-Protein Contacts for 3O8X
  • CSU: Contacts of Structural Units for 3O8X
  • Structure Factors (472 Kb)
  • Retrieve 3O8X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3O8X from S2C, [Save to disk]
  • Re-refined 3o8x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3O8X 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 3O8X
  • 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 3O8X, from MSDmotif at EBI
  • Fold representative 3o8x from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3o8x_D] [3o8x] [3o8x_B] [3o8x_A] [3o8x_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3O8X with the sequences similar proteins can be viewed for 3O8X'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 3O8X
  • Community annotation for 3O8X 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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