6M9T

Crystal structure of EP3 receptor bound to misoprostol-FA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of misoprostol bound to the labor inducer prostaglandin E2receptor.

Audet, M.White, K.L.Breton, B.Zarzycka, B.Han, G.W.Lu, Y.Gati, C.Batyuk, A.Popov, P.Velasquez, J.Manahan, D.Hu, H.Weierstall, U.Liu, W.Shui, W.Katritch, V.Cherezov, V.Hanson, M.A.Stevens, R.C.

(2019) Nat Chem Biol 15: 11-17

  • DOI: 10.1038/s41589-018-0160-y
  • Primary Citation of Related Structures:  
    6M9T

  • PubMed Abstract: 
  • Misoprostol is a life-saving drug in many developing countries for women at risk of post-partum hemorrhaging owing to its affordability, stability, ease of administration and clinical efficacy. However, misoprostol lacks receptor and tissue selectivities, and thus its use is accompanied by a number of serious side effects ...

    Misoprostol is a life-saving drug in many developing countries for women at risk of post-partum hemorrhaging owing to its affordability, stability, ease of administration and clinical efficacy. However, misoprostol lacks receptor and tissue selectivities, and thus its use is accompanied by a number of serious side effects. The development of pharmacological agents combining the advantages of misoprostol with improved selectivity is hindered by the absence of atomic details of misoprostol action in labor induction. Here, we present the 2.5 Å resolution crystal structure of misoprostol free-acid form bound to the myometrium labor-inducing prostaglandin E 2 receptor 3 (EP3). The active state structure reveals a completely enclosed binding pocket containing a structured water molecule that coordinates misoprostol's ring structure. Modeling of selective agonists in the EP3 structure reveals rationales for selectivity. These findings will provide the basis for the next generation of uterotonic drugs that will be suitable for administration in low resource settings.


    Organizational Affiliation

    Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA. stevens@usc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Prostaglandin E2 receptor EP3 subtype, Endolysin chimeraA537Homo sapiensEscherichia virus T4Mutation(s): 6 
Gene Names: PTGER3
EC: 3.2.1.17
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
prostaglandin E2 receptor with bound misoprostol
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P43115 (Homo sapiens)
Explore P43115 
Go to UniProtKB:  P43115
NIH Common Fund Data Resources
PHAROS  P43115
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J9P
Query on J9P

Download CCD File 
A
(11alpha,12alpha,13E,16S)-11,16-dihydroxy-16-methyl-9-oxoprost-13-en-1-oic acid
C21 H36 O5
CNWGPXZGIIOYDL-AGRNYGATSA-N
 Ligand Interaction
OLC
Query on OLC

Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
OLA
Query on OLA

Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.8α = 90
b = 54.85β = 95.83
c = 96.8γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.2: 2020-04-29
    Changes: Data collection