3DZY Transcription Dna date Jul 30, 2008
title Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On Dn With Rosiglitazone, 9-Cis Retinoic Acid And Ncoa2 Peptide
authors V.Chandra, P.Huang, Y.Hamuro, S.Raghuram, Y.Wang, T.P.Burris, F.Ra
compound source
Molecule: Retinoic Acid Receptor Rxr-Alpha
Chain: A
Fragment: Unp Residues 11-462
Synonym: Retinoid X Receptor Alpha, Nuclear Receptor Subfam Group B Member 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rxra, Nr2b1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-46 Eklic

Molecule: Peroxisome Proliferator-Activated Receptor Gamma
Chain: D
Fragment: Unp Residues 102-505
Synonym: Ppar-Gamma, Nuclear Receptor Subfamily 1 Group C M
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pparg, Nr1c3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-46 Eklic

Molecule: Dna (5'- D(Dcpdapdapdapdcpdtpdapdgpdgpdtpdcpdapdapdap Pdcpdapdg)-3');
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna

Molecule: Dna (5'- D(Dcpdtpdgpdapdcpdcpdtpdtpdtpdgpdapdcpdcpdtp Pdtpdtpdg)-3');
Chain: F
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna

Molecule: Ncoa2 Peptide
Chain: G, E
Engineered: Yes
Other_details: Lxxll Motif Peptide

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Humans
symmetry Space Group: P 1 21 1
R_factor 0.213 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.803 146.514 67.223 90.00 115.59 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand 9CR, BRL, ZN BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • steroid hormone receptor act...


  • D


    Primary referenceStructure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA., Chandra V, Huang P, Hamuro Y, Raghuram S, Wang Y, Burris TP, Rastinejad F, Nature. 2008 Nov 20;456(7220):350-6. PMID:19043829
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (124 Kb) [Save to disk]
  • Biological Unit Coordinates (3dzy.pdb1.gz) 116 Kb
  • LPC: Ligand-Protein Contacts for 3DZY
  • CSU: Contacts of Structural Units for 3DZY
  • Likely Quarternary Molecular Structure file(s) for 3DZY
  • Structure Factors (906 Kb)
  • Retrieve 3DZY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DZY from S2C, [Save to disk]
  • Re-refined 3dzy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DZY 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 3DZY
  • 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
  • 3D motif for 3DZY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dzy] [3dzy_A] [3dzy_E] [3dzy_G] [3dzy_C] [3dzy_F] [3dzy_D]
  • SWISS-PROT database: [Q15596] [P37231] [P19793]
  • Domain organization of [NCOA2_HUMAN] [PPARG_HUMAN] [RXRA_HUMAN] by SWISSPFAM
  • Domains found in 3DZY: [HOLI] [ZnF_C4 ] by SMART
  • Other resources with information on 3DZY
  • Community annotation for 3DZY 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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