6M9T

Crystal structure of EP3 receptor bound to misoprostol-FA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • 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 selectivi ...

    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

    Department of Structural Biology, School of Medicine, Stanford University, Palo Alto, CA, USA.,Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA.,Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA. stevens@usc.edu.,Moscow Institute of Physics & Technology, Dolgoprudn, Russia.,Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,iHuman Institute, ShanghaiTech University, Shanghai, China.,GPCR Consortium, San Marcos, CA, USA.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Skolkovo Institute of Science and Technology, Moscow, Russia.,Biodesign Center for Applied Structural Discovery, Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.,Domain Therapeutics NA Inc., Montreal, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prostaglandin E2 receptor EP3 subtype, Endolysin chimera
A
537Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 4 
Gene Names: PTGER3, E
EC: 3.2.1.17
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
prostaglandin E2 receptor with bound misoprostol
Find proteins for P43115 (Homo sapiens)
Go to Gene View: PTGER3
Go to UniProtKB:  P43115
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
OLA
Query on OLA

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Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
J9P
Query on J9P

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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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 120.800α = 90.00
b = 54.850β = 95.83
c = 96.800γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata reduction
BUSTERrefinement
PHASERphasing
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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