3FUB Hormone date Jan 14, 2009
title Crystal Structure Of Gdnf-Gfralpha1 Complex
authors V.Parkash, A.Goldman
compound source
Molecule: Gdnf Family Receptor Alpha-1
Chain: A, C
Fragment: Sequence Database Residues 145-425
Synonym: Gfr-Alpha-1, Gdnf Receptor Alpha, Gdnfr-Alpha, Tgf Related Neurotrophic Factor Receptor 1, Ret Ligand 1;
Organism_scientific: Rattus Norvegicus
Organism_common: Rat
Organism_taxid: 10116

Molecule: Glial Cell Line-Derived Neurotrophic Factor
Chain: B, D
Synonym: Astrocyte-Derived Trophic Factor, Atf, Hgdnf
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gdnf
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac
symmetry Space Group: C 1 2 1
R_factor 0.226 R_Free 0.280
length a length b length c angle alpha angle beta angle gamma
45.200 84.100 179.200 90.00 96.10 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand EDO, NAG, SO4 enzyme
A, C

D, B

Primary referenceComparison of GFL-GFRalpha complexes: further evidence relating GFL bend angle to RET signalling., Parkash V, Goldman A, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jun 1;65(Pt, 6):551-8. Epub 2009 May 23. PMID:19478429
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk]
  • Biological Unit Coordinates (3fub.pdb1.gz) 94 Kb
  • Biological Unit Coordinates (3fub.pdb2.gz) 98 Kb
  • LPC: Ligand-Protein Contacts for 3FUB
  • CSU: Contacts of Structural Units for 3FUB
  • Likely Quarternary Molecular Structure file(s) for 3FUB
  • Structure Factors (244 Kb)
  • Retrieve 3FUB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FUB from S2C, [Save to disk]
  • Re-refined 3fub structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3FUB 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 3FUB
  • 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 3FUB, from MSDmotif at EBI
  • Fold representative 3fub from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fub_D] [3fub_B] [3fub] [3fub_A] [3fub_C]
  • SWISS-PROT database: [P39905] [Q62997]
  • Domain organization of [GDNF_HUMAN] [GFRA1_RAT] by SWISSPFAM
  • Domains found in 3FUB: [GDNF] [TGFB ] by SMART
  • Other resources with information on 3FUB
  • Community annotation for 3FUB 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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