4JGV Transcription date Mar 04, 2013
title Crystal Structure Of Human Nur77 Ligand-Binding Domain In Co Thpn
authors Q.Zhang, F.Li, A.Li, X.Tian, W.Wan, Y.Wan, H.Chen, Y.Xing, Q.Wu, T.Li
compound source
Molecule: Nuclear Receptor Subfamily 4 Group A Member 1
Chain: A, B
Fragment: Ligand Binding Domain, Unp Residues 351-598
Synonym: Early Response Protein Nak1, Nuclear Hormone Recep Nur77, Nur77, Orphan Nuclear Receptor Hmr, Orphan Nuclear Tr3, St-59, Testicular Receptor 3;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr4a1, Gfrp1, Hmr, Nak1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: P 21 21 21
R_factor 0.178 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.084 76.900 128.137 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.01 Å
ligand GOL, T94 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceOrphan nuclear receptor TR3 acts in autophagic cell death via mitochondrial signaling pathway., Wang WJ, Wang Y, Chen HZ, Xing YZ, Li FW, Zhang Q, Zhou B, Zhang HK, Zhang J, Bian XL, Li L, Liu Y, Zhao BX, Chen Y, Wu R, Li AZ, Yao LM, Chen P, Zhang Y, Tian XY, Beermann F, Wu M, Han J, Huang PQ, Lin T, Wu Q, Nat Chem Biol. 2014 Feb;10(2):133-40. doi: 10.1038/nchembio.1406. Epub 2013 Dec, 8. PMID:24316735
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (85 Kb) [Save to disk]
  • Biological Unit Coordinates (4jgv.pdb1.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 4JGV
  • CSU: Contacts of Structural Units for 4JGV
  • Structure Factors (191 Kb)
  • Retrieve 4JGV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JGV from S2C, [Save to disk]
  • Re-refined 4jgv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JGV 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 4JGV
  • 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 4JGV, from MSDmotif at EBI
  • Fold representative 4jgv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jgv_A] [4jgv_B] [4jgv]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4JGV: [HOLI ] by SMART
  • Other resources with information on 4JGV
  • Community annotation for 4JGV at PDBWiki (http://pdbwiki.org)

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