6ME8

XFEL crystal structure of human melatonin receptor MT2 (N86D) in complex with 2-phenylmelatonin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    6ME7, 6ME6, 6ME9, 6ME8

  • 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 ...

    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

    Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA. cherezov@usc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin AB460Escherichia coliHomo sapiensClostridium pasteurianumMutation(s): 11 
Gene Names: cybCMTNR1B
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors: Class A
Protein: 
MT2 melatonin receptor with bound 2-phenylmelatonin
Find proteins for P49286 (Homo sapiens)
Explore P49286 
Go to UniProtKB:  P49286
NIH Common Fund Data Resources
PHAROS:  P49286
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P00268 (Clostridium pasteurianum)
Explore P00268 
Go to UniProtKB:  P00268
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JEY
Query on JEY

Download Ideal Coordinates CCD File 
A, B
N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide
C19 H20 N2 O2
OFCLARYYBGKCHN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.7α = 90
b = 145.8β = 107.4
c = 77γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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