1YJE Transcription date Jan 14, 2005
title Crystal Structure Of The Rngfi-B Ligand-Binding Domain
authors R.Flaig, H.Greschik, C.Peluso-Iltis, D.Moras, Structural Proteom Europe (Spine)
compound source
Molecule: Orphan Nuclear Receptor Nr4a1
Chain: A
Fragment: Ligand-Binding Domain
Synonym: Orphan Nuclear Receptor Hmr, Nerve Growth Factor I Protein I-B, Ngfi-B, Nur77, Rngfi-B;
Engineered: Yes
Organism_scientific: Rattus Norvegicus
Organism_common: Norway Rat
Organism_taxid: 10116
Gene: Nr4a1, Hmr, Ngfib
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15b
symmetry Space Group: I 41 2 2
R_factor 0.243 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.422 90.422 140.637 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
related structures by homologous chain: 1OVL
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural Basis for the Cell-specific Activities of the NGFI-B and the Nurr1 Ligand-binding Domain., Flaig R, Greschik H, Peluso-Iltis C, Moras D, J Biol Chem 2005 May 13;280(19):19250-8. Epub 2005 Feb 16. PMID:15716272
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk]
  • Biological Unit Coordinates (1yje.pdb1.gz) 36 Kb
  • CSU: Contacts of Structural Units for 1YJE
  • Likely Quarternary Molecular Structure file(s) for 1YJE
  • Structure Factors (115 Kb)
  • Retrieve 1YJE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YJE from S2C, [Save to disk]
  • Re-refined 1yje structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YJE 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 1YJE
  • 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 1YJE, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yje_A] [1yje]
  • SWISS-PROT database: [P22829]
  • Domain organization of [NR4A1_RAT] by SWISSPFAM
  • Domain found in 1YJE: [HOLI ] by SMART
  • Other resources with information on 1YJE
  • Community annotation for 1YJE 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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