4DM8 Transcription Protein Binding date Feb 07, 2012
title Crystal Structure Of Rarb Lbd In Complex With 9cis Retinoic
authors J.Osz, Y.Br Livet, C.Peluso-Iltis, V.Cura, S.Eiler, M.Ruff, W.Bour N.Rochel, D.Moras
compound source
Molecule: Retinoic Acid Receptor Beta
Chain: A, B
Fragment: Unp Residues 176-421
Synonym: Rar-Beta, Hbv-Activated Protein, Nuclear Receptor Group B Member 2, Rar-Epsilon;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rarb, Hap, Nr1b2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Nuclear Receptor Coactivator 1
Chain: C, D
Fragment: Unp Residues 676-700
Synonym: Ncoa-1, Class E Basic Helix-Loop-Helix Protein 74, Protein Hin-2, Rip160, Renal Carcinoma Antigen Ny-Ren-52, S Receptor Coactivator 1, Src-1;
Ec: 2.3.1.48
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Synthetic Peptide
symmetry Space Group: P 21 21 21
R_factor 0.224 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.482 83.622 108.779 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand REA BindingDB enzyme Transferase E.C.2.3.1.48 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


Primary referenceStructural basis for a molecular allosteric control mechanism of cofactor binding to nuclear receptors., Osz J, Brelivet Y, Peluso-Iltis C, Cura V, Eiler S, Ruff M, Bourguet W, Rochel N, Moras D, Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):E588-94. Epub 2012 Feb 21. PMID:22355136
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (88 Kb) [Save to disk]
  • Biological Unit Coordinates (4dm8.pdb1.gz) 42 Kb
  • Biological Unit Coordinates (4dm8.pdb2.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 4DM8
  • CSU: Contacts of Structural Units for 4DM8
  • Structure Factors (198 Kb)
  • Retrieve 4DM8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DM8 from S2C, [Save to disk]
  • Re-refined 4dm8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DM8 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 4DM8
  • 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 4DM8, from MSDmotif at EBI
  • Fold representative 4dm8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dm8] [4dm8_D] [4dm8_B] [4dm8_A] [4dm8_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4DM8: [HOLI ] by SMART
  • Other resources with information on 4DM8
  • Community annotation for 4DM8 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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