6ME4

XFEL crystal structure of human melatonin receptor MT1 in complex with 2-iodomelatonin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of ligand recognition at the human MT1melatonin receptor.

Stauch, B.Johansson, L.C.McCorvy, J.D.Patel, N.Han, G.W.Huang, X.P.Gati, C.Batyuk, A.Slocum, S.T.Ishchenko, A.Brehm, W.White, T.A.Michaelian, N.Madsen, C.Zhu, L.Grant, T.D.Grandner, J.M.Shiriaeva, A.Olsen, R.H.J.Tribo, A.R.Yous, S.Stevens, R.C.Weierstall, U.Katritch, V.Roth, B.L.Liu, W.Cherezov, V.

(2019) Nature 569: 284-288

  • DOI: 10.1038/s41586-019-1141-3
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Melatonin (N-acetyl-5-methoxytryptamine) is a neurohormone that maintains circadian rhythms <sup>1 </sup> by synchronization to environmental cues and is involved in diverse physiological processes <sup>2 </sup> such as the regulation of blood pressu ...

    Melatonin (N-acetyl-5-methoxytryptamine) is a neurohormone that maintains circadian rhythms 1 by synchronization to environmental cues and is involved in diverse physiological processes 2 such as the regulation of blood pressure and core body temperature, oncogenesis, and immune function 3 . Melatonin is formed in the pineal gland in a light-regulated manner 4 by enzymatic conversion from 5-hydroxytryptamine (5-HT or serotonin), and modulates sleep and wakefulness 5 by activating two high-affinity G-protein-coupled receptors, type 1A (MT 1 ) and type 1B (MT 2 ) 3,6 . Shift work, travel, and ubiquitous artificial lighting can disrupt natural circadian rhythms; as a result, sleep disorders affect a substantial population in modern society and pose a considerable economic burden 7 . Over-the-counter melatonin is widely used to alleviate jet lag and as a safer alternative to benzodiazepines and other sleeping aids 8,9 , and is one of the most popular supplements in the United States 10 . Here, we present high-resolution room-temperature X-ray free electron laser (XFEL) structures of MT 1 in complex with four agonists: the insomnia drug ramelteon 11 , two melatonin analogues, and the mixed melatonin-serotonin antidepressant agomelatine 12,13 . The structure of MT 2 is described in an accompanying paper 14 . Although the MT 1 and 5-HT receptors have similar endogenous ligands, and agomelatine acts on both receptors, the receptors differ markedly in the structure and composition of their ligand pockets; in MT 1 , access to the ligand pocket is tightly sealed from solvent by extracellular loop 2, leaving only a narrow channel between transmembrane helices IV and V that connects it to the lipid bilayer. The binding site is extremely compact, and ligands interact with MT 1 mainly by strong aromatic stacking with Phe179 and auxiliary hydrogen bonds with Asn162 and Gln181. Our structures provide an unexpected example of atypical ligand entry for a non-lipid receptor, lay the molecular foundation of ligand recognition by melatonin receptors, and will facilitate the design of future tool compounds and therapeutic agents, while their comparison to 5-HT receptors yields insights into the evolution and polypharmacology of G-protein-coupled receptors.


    Organizational Affiliation

    Hauptman-Woodward Institute, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA, USA.,Department of Physics, Arizona State University, Tempe, AZ, USA.,Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA. cherezov@usc.edu.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Center for Free-Electron Laser Science, DESY, Hamburg, Germany.,Stanford University, Department of Structural Biology, 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.,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.,SLAC National Accelerator Laboratory, Bioscience Division, Menlo Park, CA, USA.,Univ Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, France.,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.,Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.,School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA. w.liu@asu.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
chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase
A
503Pyrococcus abyssi (strain GE5 / Orsay)Homo sapiens
This entity is chimeric
Mutation(s): 9 
Gene Names: MTNR1A
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V2J8
Find proteins for P48039 (Homo sapiens)
Go to Gene View: MTNR1A
Go to UniProtKB:  P48039
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ML2
Query on ML2

Download SDF File 
Download CCD File 
A
N-[2-(2-iodo-5-methoxy-1H-indol-3-yl)ethyl]acetamide
C13 H15 I N2 O2
FJDDSMSDZHURBJ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 122.600α = 90.00
b = 122.600β = 90.00
c = 123.300γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

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