8QJ2 | pdb_00008qj2

Structure of active state MC4R in complex with a potent ligand mimicking nanobody


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure elucidation of a human melanocortin-4 receptor specific orthosteric nanobody agonist.

Fontaine, T.Busch, A.Laeremans, T.De Cesco, S.Liang, Y.L.Jaakola, V.P.Sands, Z.Triest, S.Masiulis, S.Dekeyzer, L.Samyn, N.Loeys, N.Perneel, L.Debaere, M.Martini, M.Vantieghem, C.Virmani, R.Skieterska, K.Staelens, S.Barroco, R.Van Roy, M.Menet, C.

(2024) Nat Commun 15: 7029-7029

  • DOI: https://doi.org/10.1038/s41467-024-50827-7
  • Primary Citation of Related Structures:  
    8QJ2

  • PubMed Abstract: 

    The melanocortin receptor 4 (MC4R) belongs to the melanocortin receptor family of G-protein coupled receptors and is a key switch in the leptin-melanocortin molecular axis that controls hunger and satiety. Brain-produced hormones such as α-melanocyte-stimulating hormone (agonist) and agouti-related peptide (inverse agonist) regulate the molecular communication of the MC4R axis but are promiscuous for melanocortin receptor subtypes and induce a wide array of biological effects. Here, we use a chimeric construct of conformation-selective, nanobody-based binding domain (a ConfoBody Cb80) and active state-stabilized MC4R-β2AR hybrid for efficient de novo discovery of a sequence diverse panel of MC4R-specific, potent and full agonistic nanobodies. We solve the active state MC4R structure in complex with the full agonistic nanobody pN162 at 3.4 Å resolution. The structure shows a distinct interaction with pN162 binding deeply in the orthosteric pocket. MC4R peptide agonists, such as the marketed setmelanotide, lack receptor selectivity and show off-target effects. In contrast, the agonistic nanobody is highly specific and hence can be a more suitable agent for anti-obesity therapeutic intervention via MC4R.


  • Organizational Affiliation

    Confo Therapeutics N.V, Ghent, Belgium.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortA [auth B]394Homo sapiensMutation(s): 9 
Gene Names: GNAS
EC: 3.6.5
Membrane Entity: Yes 
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Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B [auth C]350Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody-35D [auth N]138Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Melanocortin receptor 4,Red fluorescent protein drFP583E [auth A]729Escherichia coliHomo sapiensDiscosoma sp.
This entity is chimeric
Mutation(s): 32 
Gene Names: cybCMC4R
Membrane Entity: Yes 
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Find proteins for P32245 (Homo sapiens)
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PHAROS:  P32245
GTEx:  ENSG00000166603 
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UniProt GroupsQ9U6Y8P0ABE7P32245
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
pN162F [auth D]117Lama glamaMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentBelgium2016-R-49
Other governmentBelgiumHBC_2020.2042

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-04-23
    Changes: Data collection, Database references