5VZ3 Signaling Protein date May 26, 2017
title Growth Factor Crystal Structure At 1.97 Angstrom Resolution
authors D.Lakshminarasimhan, A.White, R.K.Suto
compound source
Molecule: Growthdifferentiation Factor 15
Chain: A
Fragment: Unp Residues 197-308
Synonym: Gdf-15, Macrophage Inhibitory Cytokine 1, Mic-1, N Activated Gene 1 Protein, Nag-1, Nsaid-Regulated Gene 1 Pro 1, Placental Tgf-Beta, Placental Bone Morphogenetic Protein Differentiation Factor;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gdf15, Mic1, Pdf, Plab, Ptgfb
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Expi293f
symmetry Space Group: C 2 2 2
R_factor 0.194 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.964 123.020 41.698 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.97 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceNon-homeostatic body weight regulation through a brainstem-restricted receptor for GDF15., Hsu JY, Crawley S, Chen M, Ayupova DA, Lindhout DA, Higbee J, Kutach A, Joo W, Gao Z, Fu D, To C, Mondal K, Li B, Kekatpure A, Wang M, Laird T, Horner G, Chan J, McEntee M, Lopez M, Lakshminarasimhan D, White A, Wang SP, Yao J, Yie J, Matern H, Solloway M, Haldankar R, Parsons T, Tang J, Shen WD, Alice Chen Y, Tian H, Allan BB, Nature. 2017 Sep 27. doi: 10.1038/nature24042. PMID:28953886
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (23 Kb) [Save to disk]
  • Biological Unit Coordinates (5vz3.pdb1.gz) 37 Kb
  • CSU: Contacts of Structural Units for 5VZ3
  • Structure Factors (85 Kb)
  • Retrieve 5VZ3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VZ3 from S2C, [Save to disk]
  • View 5VZ3 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 5VZ3
  • 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
  • Fold representative 5vz3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vz3_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VZ3
  • Community annotation for 5VZ3 at PDBWiki (http://pdbwiki.org)

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