3O9W Immune System date Aug 04, 2010
title Recognition Of A Glycolipid Antigen By The 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 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.003 188.368 149.791 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 1O2, FUC, NAG enzyme
Gene MCG
Gene
Ontology
ChainFunctionProcessComponent
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] (287 Kb) [Save to disk]
  • Biological Unit Coordinates (3o9w.pdb1.gz) 279 Kb
  • LPC: Ligand-Protein Contacts for 3O9W
  • CSU: Contacts of Structural Units for 3O9W
  • Structure Factors (428 Kb)
  • Retrieve 3O9W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3O9W from S2C, [Save to disk]
  • Re-refined 3o9w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3O9W 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 3O9W
  • 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 3O9W, from MSDmotif at EBI
  • Fold representative 3o9w from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3o9w_C] [3o9w_A] [3o9w_B] [3o9w] [3o9w_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3O9W: [IG] [IGc1] [IGv ] by SMART
  • Other resources with information on 3O9W
  • Community annotation for 3O9W 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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