7DB6

human melatonin receptor MT1 - Gi1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the human MT 1 -G i signaling complex.

Okamoto, H.H.Miyauchi, H.Inoue, A.Raimondi, F.Tsujimoto, H.Kusakizako, T.Shihoya, W.Yamashita, K.Suno, R.Nomura, N.Kobayashi, T.Iwata, S.Nishizawa, T.Nureki, O.

(2021) Nat Struct Mol Biol 28: 694-701

  • DOI: 10.1038/s41594-021-00634-1
  • Primary Citation of Related Structures:  
    7DB6

  • PubMed Abstract: 
  • Melatonin receptors (MT 1 and MT 2 ) transduce inhibitory signaling by melatonin (N-acetyl-5-methoxytryptamine), which is associated with sleep induction and circadian rhythm modulation. Although recently reported crystal structures of ligand-bound MT 1 and MT 2 elucidated the basis of ligand entry and recognition, the ligand-induced MT 1 rearrangement leading to G i -coupling remains unclear ...

    Melatonin receptors (MT 1 and MT 2 ) transduce inhibitory signaling by melatonin (N-acetyl-5-methoxytryptamine), which is associated with sleep induction and circadian rhythm modulation. Although recently reported crystal structures of ligand-bound MT 1 and MT 2 elucidated the basis of ligand entry and recognition, the ligand-induced MT 1 rearrangement leading to G i -coupling remains unclear. Here we report a cryo-EM structure of the human MT 1 -G i signaling complex at 3.3 Å resolution, revealing melatonin-induced conformational changes propagated to the G-protein-coupling interface during activation. In contrast to other G i -coupled receptors, MT 1 exhibits a large outward movement of TM6, which is considered a specific feature of G s -coupled receptors. Structural comparison of G i and G s complexes demonstrated conformational diversity of the C-terminal entry of the G i protein, suggesting loose and variable interactions at the end of the α5 helix of G i protein. These notions, together with our biochemical and computational analyses, highlight variable binding modes of Gα i and provide the basis for the selectivity of G-protein signaling.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. nureki@bs.s.u-tokyo.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1A354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63096
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B344Rattus rattusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62873
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C68Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt
Find proteins for P63212 (Bos taurus)
Explore P63212 
Go to UniProtKB:  P63212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63212
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
scFv16D [auth E]260Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Melatonin receptor type 1AE [auth D]372Homo sapiensMutation(s): 0 
Gene Names: MTNR1A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P48039 (Homo sapiens)
Explore P48039 
Go to UniProtKB:  P48039
PHAROS:  P48039
GTEx:  ENSG00000168412 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48039
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JEV (Subject of Investigation/LOI)
Query on JEV

Download Ideal Coordinates CCD File 
F [auth D]N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide
C16 H21 N O2
YLXDSYKOBKBWJQ-LBPRGKRZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references