6ME7

XFEL crystal structure of human melatonin receptor MT2 (H208A) in complex with 2-phenylmelatonin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

XFEL structures of the human MT2melatonin receptor reveal the basis of subtype selectivity.

Johansson, L.C.Stauch, B.McCorvy, J.D.Han, G.W.Patel, N.Huang, X.P.Batyuk, A.Gati, C.Slocum, S.T.Li, C.Grandner, J.M.Hao, S.Olsen, R.H.J.Tribo, A.R.Zaare, S.Zhu, L.Zatsepin, N.A.Weierstall, U.Yous, S.Stevens, R.C.Liu, W.Roth, B.L.Katritch, V.Cherezov, V.

(2019) Nature 569: 289-292

  • DOI: 10.1038/s41586-019-1144-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human MT <sub>1 </sub> and MT <sub>2 </sub> melatonin receptors <sup>1,2 </sup> are G-protein-coupled receptors (GPCRs) that help to regulate circadian rhythm and sleep patterns <sup>3 </sup>. Drug development efforts have targeted both receptors ...

    The human MT 1 and MT 2 melatonin receptors 1,2 are G-protein-coupled receptors (GPCRs) that help to regulate circadian rhythm and sleep patterns 3 . Drug development efforts have targeted both receptors for the treatment of insomnia, circadian rhythm and mood disorders, and cancer 3 , and MT 2 has also been implicated in type 2 diabetes 4,5 . Here we report X-ray free electron laser (XFEL) structures of the human MT 2 receptor in complex with the agonists 2-phenylmelatonin (2-PMT) and ramelteon 6 at resolutions of 2.8 Å and 3.3 Å, respectively, along with two structures of function-related mutants: H208 5.46 A (superscripts represent the Ballesteros-Weinstein residue numbering nomenclature 7 ) and N86 2.50 D, obtained in complex with 2-PMT. Comparison of the structures of MT 2 with a published structure 8 of MT 1 reveals that, despite conservation of the orthosteric ligand-binding site residues, there are notable conformational variations as well as differences in [ 3 H]melatonin dissociation kinetics that provide insights into the selectivity between melatonin receptor subtypes. A membrane-buried lateral ligand entry channel is observed in both MT 1 and MT 2 , but in addition the MT 2 structures reveal a narrow opening towards the solvent in the extracellular part of the receptor. We provide functional and kinetic data that support a prominent role for intramembrane ligand entry in both receptors, and suggest that there might also be an extracellular entry path in MT 2 . Our findings contribute to a molecular understanding of melatonin receptor subtype selectivity and ligand access modes, which are essential for the design of highly selective melatonin tool compounds and therapeutic agents.


    Organizational Affiliation

    Université de Lille, CHU Lille, Inserm, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, France.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA. katritch@usc.edu.,Department of Chemistry, University of Southern California, Los Angeles, CA, USA.,Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA. katritch@usc.edu.,Department of Physics, Arizona State University, Tempe, AZ, USA.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. bryan_roth@med.unc.edu.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. bryan_roth@med.unc.edu.,Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.,Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA, USA. cherezov@usc.edu.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA. cherezov@usc.edu.,Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA, USA. katritch@usc.edu.,School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. bryan_roth@med.unc.edu.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.,Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA. cherezov@usc.edu.,National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin
A, B
460Escherichia coliHomo sapiensClostridium pasteurianum
This entity is chimeric
Mutation(s): 13 
Gene Names: cybC, MTNR1B,
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P49286 (Homo sapiens)
Go to Gene View: MTNR1B
Go to UniProtKB:  P49286
Find proteins for P00268 (Clostridium pasteurianum)
Go to UniProtKB:  P00268
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
JEY
Query on JEY

Download SDF File 
Download CCD File 
A, B
N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide
2-phenylmelatonin
C19 H20 N2 O2
OFCLARYYBGKCHN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.230α = 90.00
b = 146.190β = 105.15
c = 77.340γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata reduction
PHASERphasing
BUSTERrefinement
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35 GM127026

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-08
    Type: Data collection, Database references
  • Version 1.2: 2019-05-22
    Type: Data collection, Database references