3A9E Transcription date Oct 24, 2009
title Crystal Structure Of A Mixed Agonist-Bound Rar-Alpha And Ant Bound Rxr-Alpha Heterodimer Ligand Binding Domains
authors Y.Sato, S.Duclaud, C.Peluso-Iltis, P.Poussin, D.Moras, N.Rochel
compound source
Molecule: Retinoic Acid Receptor Rxr-Alpha
Chain: A
Fragment: Ligand Binding Domain
Synonym: Retinoid X Receptor Alpha, Nuclear Receptor Subfam Group B Member 1;
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Rxra, Nr2b1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Retinoic Acid Receptor Alpha
Chain: B
Fragment: Ligand Binding Domain
Synonym: Rar-Alpha, Nuclear Receptor Subfamily 1 Group B Me
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rara, Nr1b1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: 13-Mer (Lxxll Motif) From Nuclear Receptor Coacti
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: The Peptide Was Chemically Synthesized.
symmetry Space Group: P 43 21 2
R_factor 0.201 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.300 105.300 111.338 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand 754, REA BindingDB enzyme
Primary referenceThe "Phantom Effect" of the Rexinoid LG100754: structural and functional insights., Sato Y, Ramalanjaona N, Huet T, Potier N, Osz J, Antony P, Peluso-Iltis C, Poussin-Courmontagne P, Ennifar E, Mely Y, Dejaegere A, Moras D, Rochel N, PLoS One. 2010 Nov 30;5(11):e15119. doi: 10.1371/journal.pone.0015119. PMID:21152046
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (170 Kb) [Save to disk]
  • Biological Unit Coordinates (3a9e.pdb1.gz) 164 Kb
  • Biological Unit Coordinates (3a9e.pdb2.gz) 326 Kb
  • LPC: Ligand-Protein Contacts for 3A9E
  • CSU: Contacts of Structural Units for 3A9E
  • Structure Factors (140 Kb)
  • Retrieve 3A9E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A9E from S2C, [Save to disk]
  • Re-refined 3a9e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A9E 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 3A9E
  • 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 3A9E, from MSDmotif at EBI
  • Fold representative 3a9e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a9e] [3a9e_B] [3a9e_A] [3a9e_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3A9E: [HOLI ] by SMART
  • Other resources with information on 3A9E
  • Community annotation for 3A9E 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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