5YWY Signaling Protein-Immune System date Nov 30, 2017
title Crystal Structure Of The Human Prostaglandin E Receptor Ep4 With Fab And Ono-Ae3-208
authors Y.Toyoda, K.Morimoto, R.Suno, S.Horita, S.Iwata, T.Kobayashi
compound source
Molecule: Prostaglandin E2 Receptor Ep4 Subtype,Prostagland Receptor Ep4 Subtype;
Chain: A
Synonym: Pge2 Receptor Ep4 Subtype,Prostanoid Ep4 Receptor
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ptger4, Ptger2
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108

Molecule: Heavy Chain Of Fab Fragment
Chain: H
Synonym: Fabh
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Hybrid
Expression_system_taxid: 37965

Molecule: Light Chain Of Fab Fragment
Chain: L
Synonym: Fabl
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Hybrid
Expression_system_taxid: 37965
symmetry Space Group: C 2 2 21
R_factor 0.222 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.980 390.150 79.360 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceLigand binding to human prostaglandin E receptor EP4 at the lipid-bilayer interface., Toyoda Y, Morimoto K, Suno R, Horita S, Yamashita K, Hirata K, Sekiguchi Y, Yasuda S, Shiroishi M, Shimizu T, Urushibata Y, Kajiwara Y, Inazumi T, Hotta Y, Asada H, Nakane T, Shiimura Y, Nakagita T, Tsuge K, Yoshida S, Kuribara T, Hosoya T, Sugimoto Y, Nomura N, Sato M, Hirokawa T, Kinoshita M, Murata T, Takayama K, Yamamoto M, Narumiya S, Iwata S, Kobayashi T, Nat Chem Biol. 2019 Jan;15(1):18-26. doi: 10.1038/s41589-018-0131-3. Epub 2018, Dec 3. PMID:30510193
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (248 Kb) [Save to disk]
  • Biological Unit Coordinates (5ywy.pdb1.gz) 241 Kb
  • CSU: Contacts of Structural Units for 5YWY
  • Structure Factors (471 Kb)
  • Retrieve 5YWY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YWY from S2C, [Save to disk]
  • View 5YWY 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 5YWY
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5ywy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ywy_L] [5ywy_H] [5ywy_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YWY
  • Community annotation for 5YWY at PDBWiki (http://pdbwiki.org)

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