2V5E Receptor Glycoprotein Complex date Oct 03, 2008
title The Structure Of The Gdnf:Coreceptor Complex: Insights Into Signalling And Heparin Binding.
authors V.Parkash, V.M.Leppanen, H.Virtanen, J.M.Jurvansuu, M.M.Bespal Y.A.Sidorova, P.Runeberg-Roos, M.Saarma, A.Goldman
compound source
Molecule: Gdnf Family Receptor Alpha-1
Chain: A
Fragment: Residues 150-349
Synonym: Gfr-Alpha-1, Gdnf Receptor Alpha, Gdnfr-Alpha, Tgf Related Neurotrophic Factor Receptor 1, Ret Ligand 1;
Engineered: Yes
Organism_scientific: Rattus Norvegicus
Organism_common: Norway Rat
Organism_taxid: 10116
Expression_system: Spodoptera Frugiperda Expression_system_common_fall Armyworm;
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac

Molecule: Glial Cell Line-Derived Neurotrophic Factor
Chain: B
Fragment: Residues 111-211
Synonym: Astrocyte-Derived Trophic Factor, Hgdnf, Atf
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda Expression_system_common_fall Armyworm;
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac
symmetry Space Group: C 1 2 1
R_factor 0.184 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.900 75.700 105.500 90.00 91.90 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand EDO, GU4, NAG, YYJ enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceThe structure of the GDNF:Coreceptor complex: Insights into RET signalling and heparin binding., Parkash V, Leppanen VM, Virtanen H, Jurvansuu JM, Bespalov MM, Sidorova YA, Runeberg-Roos P, Saarma M, Goldman A, J Biol Chem. 2008 Oct 8. PMID:18845535
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (2v5e.pdb1.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 2V5E
  • CSU: Contacts of Structural Units for 2V5E
  • Likely Quarternary Molecular Structure file(s) for 2V5E
  • Structure Factors (153 Kb)
  • Retrieve 2V5E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2V5E from S2C, [Save to disk]
  • Re-refined 2v5e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2V5E 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 2V5E
  • 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 2V5E, from MSDmotif at EBI
  • Fold representative 2v5e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2v5e_A] [2v5e_B] [2v5e]
  • SWISS-PROT database: [P39905] [Q62997]
  • Domain organization of [GDNF_HUMAN] [GFRA1_RAT] by SWISSPFAM
  • Domains found in 2V5E: [GDNF] [TGFB ] by SMART
  • Other resources with information on 2V5E
  • Community annotation for 2V5E 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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