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 Diffraction	resolution	2.80 Å
ligand	1O2, FUC, NAG	enzyme
Gene	MCG
Gene Ontology	Chain Function Process Component A protein binding endogenous lipid antigen bin... T cell receptor binding positive regulation of T cel... antigen processing and prese... positive regulation of macro... positive thymic T cell selec... positive regulation of inter... positive regulation of inter... innate immune response positive regulation of inter... antigen processing and prese... regulation of immune respons... positive regulation of NK T ... positive regulation of NK T ... lysosome lysosomal membrane endosome early endosome late endosome plasma membrane external side of plasma memb... endosome membrane membrane integral to membrane B protein binding positive regulation of T cel... response to molecule of bact... antigen processing and prese... antigen processing and prese... cellular defense response T cell differentiation in th... protein refolding response to drug response to cadmium ion extracellular region extracellular space external side of plasma memb... phagocytic vesicle membrane MHC class I protein complex
Primary reference	The 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [3o9w_B] [3o9w_C] [3o9w_D] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3O9W with the sequences similar proteins can be viewed for 3O9W'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 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.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2010 Bioinformatics Unit Weizmann Institute of Science

---