XFEL crystal structure of human melatonin receptor MT2 in complex with ramelteon

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 

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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: https://doi.org/10.1038/s41586-019-1144-0
  • Primary Citation of Related Structures:  
    6ME6, 6ME7, 6ME8, 6ME9

  • PubMed Abstract: 

    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

    Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin
A, B
460Escherichia coliHomo sapiensClostridium pasteurianumMutation(s): 12 
Gene Names: cybCMTNR1B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P49286 (Homo sapiens)
Explore P49286 
Go to UniProtKB:  P49286
PHAROS:  P49286
GTEx:  ENSG00000134640 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P00268 (Clostridium pasteurianum)
Explore P00268 
Go to UniProtKB:  P00268
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00268P0ABE7P49286
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.4α = 90
b = 145.7β = 106.2
c = 77.2γ = 90
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM127026

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2020-04-29
    Changes: Data collection
  • Version 1.5: 2023-10-11
    Changes: Data collection, Database references, Refinement description