7W0M

Cryo-EM structure of a monomeric GPCR-Gi complex with small molecule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insight into apelin receptor-G protein stoichiometry.

Yue, Y.Liu, L.Wu, L.J.Wu, Y.Wang, L.Li, F.Liu, J.Han, G.W.Chen, B.Lin, X.Brouillette, R.L.Breault, E.Longpre, J.M.Shi, S.Lei, H.Sarret, P.Stevens, R.C.Hanson, M.A.Xu, F.

(2022) Nat Struct Mol Biol 29: 688-697

  • DOI: https://doi.org/10.1038/s41594-022-00797-5
  • Primary Citation of Related Structures:  
    7SUS, 7W0L, 7W0M, 7W0N, 7W0O, 7W0P

  • PubMed Abstract: 

    The technique of cryogenic-electron microscopy (cryo-EM) has revolutionized the field of membrane protein structure and function with a focus on the dominantly observed molecular species. This report describes the structural characterization of a fully active human apelin receptor (APJR) complexed with heterotrimeric G protein observed in both 2:1 and 1:1 stoichiometric ratios. We use cryo-EM single-particle analysis to determine the structural details of both species from the same sample preparation. Protein preparations, in the presence of the endogenous peptide ligand ELA or a synthetic small molecule, both demonstrate these mixed stoichiometric states. Structural differences in G protein engagement between dimeric and monomeric APJR suggest a role for the stoichiometry of G protein-coupled receptor- (GPCR-)G protein coupling on downstream signaling and receptor pharmacology. Furthermore, a small, hydrophobic dimer interface provides a starting framework for additional class A GPCR dimerization studies. Together, these findings uncover a mechanism of versatile regulation through oligomerization by which GPCRs can modulate their signaling.


  • Organizational Affiliation

    iHuman Institute, ShanghaiTech University, Shanghai, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1356Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
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Find proteins for P63096 (Homo sapiens)
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Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1340Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
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-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Apelin receptorD [auth R]477Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: cybCAPLNRAGTRL1APJ
Membrane Entity: Yes 
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Find proteins for P0ABE7 (Escherichia coli)
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Go to UniProtKB:  P0ABE7
Find proteins for P35414 (Homo sapiens)
Explore P35414 
Go to UniProtKB:  P35414
PHAROS:  P35414
GTEx:  ENSG00000134817 
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UniProt GroupsP0ABE7P35414
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16E [auth S]297Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8EH (Subject of Investigation/LOI)
Query on 8EH

Download Ideal Coordinates CCD File 
F [auth R](1R,2S)-N-[4-(2,6-dimethoxyphenyl)-5-(6-methylpyridin-2-yl)-1,2,4-triazol-3-yl]-1-(5-methylpyrimidin-2-yl)-1-oxidanyl-propane-2-sulfonamide
C24 H27 N7 O5 S
HNGYVRSMVVCWGF-KKSFZXQISA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
8EH BindingDB:  7W0M EC50: 2.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release