7F58 | pdb_00007f58

Cryo-EM structure of THIQ-MC4R-Gs_Nb35 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7F58

This is version 1.3 of the entry. See complete history

Literature

Structural insights into ligand recognition and activation of the melanocortin-4 receptor.

Zhang, H.Chen, L.N.Yang, D.Mao, C.Shen, Q.Feng, W.Shen, D.D.Dai, A.Xie, S.Zhou, Y.Qin, J.Sun, J.P.Scharf, D.H.Hou, T.Zhou, T.Wang, M.W.Zhang, Y.

(2021) Cell Res 31: 1163-1175

  • DOI: https://doi.org/10.1038/s41422-021-00552-3
  • Primary Citation Related Structures: 
    7F53, 7F54, 7F55, 7F58

  • PubMed Abstract: 

    Melanocortin-4 receptor (MC4R) plays a central role in the regulation of energy homeostasis. Its high sequence similarity to other MC receptor family members, low agonist selectivity and the lack of structural information concerning MC4R-specific activation have hampered the development of MC4R-seletive therapeutics to treat obesity. Here, we report four high-resolution structures of full-length MC4R in complex with the heterotrimeric G s protein stimulated by the endogenous peptide ligand α-MSH, FDA-approved drugs afamelanotide (Scenesse™) and bremelanotide (Vyleesi™), and a selective small-molecule ligand THIQ, respectively. Together with pharmacological studies, our results reveal the conserved binding mode of peptidic agonists, the distinctive molecular details of small-molecule agonist recognition underlying receptor subtype selectivity, and a distinct activation mechanism for MC4R, thereby offering new insights into G protein coupling. Our work may facilitate the discovery of selective therapeutic agents targeting MC4R.


  • Organizational Affiliation
    • Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.

Macromolecule Content 

  • Total Structure Weight: 164.27 kDa 
  • Atom Count: 8,065 
  • Modeled Residue Count: 1,021 
  • Deposited Residue Count: 1,468 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Melanocortin receptor 4A [auth R]507Homo sapiensMutation(s): 0 
Gene Names: MC4R
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P32245 (Homo sapiens)
Explore P32245 
Go to UniProtKB:  P32245
PHAROS:  P32245
GTEx:  ENSG00000166603 
Entity Groups
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UniProt GroupP32245
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortB [auth A]380Homo sapiensMutation(s): 8 
Gene Names: GNASGNAS1GSP
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
Entity Groups
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UniProt GroupP63092
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]384Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups
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UniProt GroupP62873
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
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UniProt GroupP59768
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody35E [auth N]126synthetic constructMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1I8

Query on 1I8



Download:Ideal Coordinates CCD File
F [auth R](3R)-N-[(2R)-3-(4-chlorophenyl)-1-[4-cyclohexyl-4-(1,2,4-triazol-1-ylmethyl)piperidin-1-yl]-1-oxidanylidene-propan-2-yl]-1,2,3,4-tetrahydroisoquinoline-3-carboxamide
C33 H41 Cl N6 O2
HLCHESOMJVGDSJ-LOYHVIPDSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth R]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1I8 BindingDB:  7F58 Ki: min: 3, max: 646 (nM) from 5 assay(s)
IC50: min: 0.6, max: 9 (nM) from 3 assay(s)
EC50: min: 1, max: 49 (nM) from 9 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-07-02
    Changes: Data collection