8XWP

Cryo-EM structure of ET-1 bound ETBR-DNGI complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 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

Structure of endothelin ET B receptor-G i complex in a conformation stabilized by unique NPxxL motif.

Tani, K.Maki-Yonekura, S.Kanno, R.Negami, T.Hamaguchi, T.Hall, M.Mizoguchi, A.Humbel, B.M.Terada, T.Yonekura, K.Doi, T.

(2024) Commun Biol 7: 1303-1303

  • DOI: https://doi.org/10.1038/s42003-024-06905-z
  • Primary Citation of Related Structures:  
    8XWP, 8XWQ, 8ZRT

  • PubMed Abstract: 

    Endothelin type B receptor (ET B R) plays a crucial role in regulating blood pressure and humoral homeostasis, making it an important therapeutic target for related diseases. ET B R activation by the endogenous peptide hormones endothelin (ET)-1-3 stimulates several signaling pathways, including G s , G i/o , G q/11 , G 12/13 , and β-arrestin. Although the conserved NPxxY motif in transmembrane helix 7 (TM7) is important during GPCR activation, ET B R possesses the lesser known NPxxL motif. In this study, we present the cryo-EM structure of the ET B R-G i complex, complemented by MD simulations and functional studies. These investigations reveal an unusual movement of TM7 to the intracellular side during ET B R activation and the essential roles of the diverse NPxxL motif in stabilizing the active conformation of ET B R and organizing the assembly of the binding pocket for the α5 helix of G i protein. These findings enhance our understanding of the interactions between GPCRs and G proteins, thereby advancing the development of therapeutic strategies.


  • Organizational Affiliation

    Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan. ktani@ccs.tsukuba.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endothelin receptor type BA [auth R]346Homo sapiensMutation(s): 0 
Gene Names: EDNRBETRB
Membrane Entity: Yes 
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PHAROS:  P24530
GTEx:  ENSG00000136160 
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UniProt GroupP24530
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Endothelin-1B [auth L]21Homo sapiensMutation(s): 0 
Gene Names: EDN1
Membrane Entity: Yes 
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GTEx:  ENSG00000078401 
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UniProt GroupP05305
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1C [auth A]354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
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GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth B]344Homo sapiensMutation(s): 0 
Gene Names: GNB1
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GTEx:  ENSG00000078369 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth C]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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GTEx:  ENSG00000186469 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
SCFV16F [auth D]277Mus musculusMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101118
Japan Agency for Medical Research and Development (AMED)JapanJP23ama121004
Japan Society for the Promotion of Science (JSPS)Japan20H03210

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary