5GLH

Human endothelin receptor type-B in complex with ET-1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Activation mechanism of endothelin ETB receptor by endothelin-1.

Shihoya, W., Nishizawa, T., Okuta, A., Tani, K., Dohmae, N., Fujiyoshi, Y., Nureki, O., Doi, T.

(2016) Nature 537: 363-368

  • DOI: 10.1038/nature19319
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Endothelin, a 21-amino-acid peptide, participates in various physiological processes, such as regulation of vascular tone, humoral homeostasis, neural crest cell development and neurotransmission. Endothelin and its G-protein-coupled receptor are inv ...

    Endothelin, a 21-amino-acid peptide, participates in various physiological processes, such as regulation of vascular tone, humoral homeostasis, neural crest cell development and neurotransmission. Endothelin and its G-protein-coupled receptor are involved in the development of various diseases, such as pulmonary arterial hypertension, and thus are important therapeutic targets. Here we report crystal structures of human endothelin type B receptor in the ligand-free form and in complex with the endogenous agonist endothelin-1. The structures and mutation analysis reveal the mechanism for the isopeptide selectivity between endothelin-1 and -3. Transmembrane helices 1, 2, 6 and 7 move and envelop the entire endothelin peptide, in a virtually irreversible manner. The agonist-induced conformational changes are propagated to the receptor core and the cytoplasmic G-protein coupling interface, and probably induce conformational flexibility in TM6. A comparison with the M2 muscarinic receptor suggests a shared mechanism for signal transduction in class A G-protein-coupled receptors.

    Organizational Affiliation: 

    Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endothelin Receptor Subtype-B
A
498Homo sapiens, Enterobacteria phage T4
This entity is chimeric		Mutation(s): 0 
Gene Names: EDNRB (ETRB), E
EC: 3.2.1.17
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
G Protein-Coupled Receptors (GPCRs)		Protein: 
endothelin ETB receptor with bound endothelin-1
Find proteins for P24530 (Homo sapiens)
Go to Gene View: EDNRB
Go to UniProtKB:  P24530
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide from Endothelin-1
B
21Homo sapiensMutation(s): 0 
Gene Names: EDN1
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
G Protein-Coupled Receptors (GPCRs)		Protein: 
endothelin ETB receptor with bound endothelin-1
Find proteins for P05305 (Homo sapiens)
Go to Gene View: EDN1
Go to UniProtKB:  P05305
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.234 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 72.970α = 90.00
b = 172.970β = 90.00
c = 109.350γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata processing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-09-21
    Type: Database references, Structure summary
  • Version 1.2: 2016-09-28
    Type: Database references