3FUG	Transcription Transcription Regulator	date	Jan 14, 2009
title	Crystal Structure Of The Retinoid X Receptor Ligand Binding Domain Bound To The Synthetic Agonist 3-[4-Hydroxy-3-(3,5, 5,8,8-Pentamethyl-5,6,7,8-Tetrahydronaphthalen-2-Yl)- Phenyl]Acrylic Acid
authors	W.Bourguet
compound		source
Molecule: Retinoic Acid Receptor Rxr-Alpha Chain: A Fragment: Ligand Binding Domain (Residues 223-462) Synonym: Retinoid X Receptor Alpha, Nuclear Receptor Subfamily 2 Group B Member 1; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Nr2b1, Rxra Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet15b
Molecule: Nuclear Receptor Coactivator 2 Chain: B Fragment: Nuclear Receptor Interaction Motif 2 (Residues 686-698); Synonym: Ncoa-2, Transcriptional Intermediary Factor 2, Htif2; Engineered: Yes		Synthetic: Yes Other_details: This Sequence Occurs Naturally In Humans. The Peptide Has Been Synthesized By Automatic Chemical Synthesis
symmetry	Space Group: P 43 21 2	R_factor 0.205 R_Free 0.241
crystal cell	length a length b length c angle alpha angle beta angle gamma 65.763 65.763 110.857 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	2E3	enzyme
Gene Ontology	Chain Function Process Component A DNA binding sequence-specific DNA bindin... retinoic acid receptor activ... transcription coactivator ac... ligand-activated sequence-sp... 9-cis retinoic acid receptor... protein binding transcription factor binding... enzyme binding chromatin DNA binding vitamin D receptor binding sequence-specific DNA bindin... transcription regulatory reg... retinoic acid-responsive ele... metal ion binding protein heterodimerization a... vitamin D response element b... negative regulation of trans... in utero embryonic developme... placenta development maternal placenta developmen... transcription, DNA-dependent... regulation of transcription,... regulation of transcription ... transcription initiation fro... vitamin metabolic process heart development embryo implantation cholesterol metabolic proces... gene expression virus-host interaction response to retinoic acid peroxisome proliferator acti... cellular lipid metabolic pro... small molecule metabolic pro... positive regulation of trans... positive regulation of trans... retinoic acid receptor signa... ventricular cardiac muscle t... ventricular cardiac muscle c... cardiac muscle cell prolifer... secretory columnal luminar e... regulation of branching invo... nuclear chromatin nucleus nucleoplasm
Primary reference	Modulating Retinoid X Receptor with a Series of (E)-3-[4-Hydroxy-3-(3-alkoxy-5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphtha len-2-yl)phenyl]acrylic Acids and Their 4-Alkoxy Isomers (dagger)., Santin EP, Germain P, Quillard F, Khanwalkar H, Rodriguez-Barrios F, Gronemeyer H, de Lera AR, Bourguet W, J Med Chem. 2009 May 1. PMID:19408900

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk] Biological Unit Coordinates (3fug.pdb1.gz) 39 Kb Biological Unit Coordinates (3fug.pdb2.gz) 76 Kb LPC: Ligand-Protein Contacts for 3FUG CSU: Contacts of Structural Units for 3FUG Likely Quarternary Molecular Structure file(s) for 3FUG Structure Factors (802 Kb) Retrieve 3FUG in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3FUG from S2C, [Save to disk] Re-refined 3fug structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3FUG 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 3FUG

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 3FUG, from MSDmotif at EBI Fold representative 3fug from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3fug_A] [3fug_B] SWISS-PROT database: [Q15596] [P19793] Domain organization of [NCOA2_HUMAN] [RXRA_HUMAN] by SWISSPFAM Domain found in 3FUG: [HOLI ] by SMART Alignments of the sequence of 3FUG with the sequences similar proteins can be viewed for 3FUG's classification [NCOA2_HUMAN] [RXRA_HUMAN] 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 [NCOA2_HUMAN] [RXRA_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3FUG

Community annotation for 3FUG at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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