Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.45 kDa 
• Atom Count: 3643 
• Residue Count: 473 
• Unique protein chains: 2

5GLH

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

• DOI: 10.2210/pdb5GLH/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-07-11 Released: 2016-09-07 
• Deposition Author(s): Shihoya, W., Nishizawa, T., Okuta, A., Tani, K., Fujiyoshi, Y., Dohmae, N., Nureki, O., Doi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.277 
• R-Value Work: 0.234 
• R-Value Observed: 0.238 

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

• PubMed: 27595334 
• DOI: 10.1038/nature19319
• Structures With Same Primary Citation


• 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 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.

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Organizational Affiliation: 

Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Endothelin Receptor Subtype-B	A	498	Homo sapiens	Mutation(s): 0  Gene Names: EDNRB, ETRB EC: 3.2.1.17
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs)	Protein:  endothelin ETB receptor with bound endothelin-1
Find proteins for P00720 (Enterobacteria phage T4) Go to UniProtKB:  P00720
Find proteins for P24530 (Homo sapiens) Go to UniProtKB:  P24530
NIH Common Fund Data Resources
PHAROS  P24530 GTEx  ENSG00000136160

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Peptide from Endothelin-1	B	21	Homo sapiens	Mutation(s): 0  Gene Names: EDN1
Membrane protein Mpstruc	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 UniProtKB:  P05305
NIH Common Fund Data Resources
PHAROS  P05305 GTEx  ENSG00000078401

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.277 
• R-Value Work: 0.234 
• R-Value Observed: 0.238 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.97	α = 90
b = 172.97	β = 90
c = 109.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data processing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-07-11 
• Released Date: 2016-09-07 
Deposition Author(s): Shihoya, W., Nishizawa, T., Okuta, A., Tani, K., Fujiyoshi, Y., Dohmae, N., Nureki, O., Doi, T.

Revision History 

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Database references, Structure summary
• Version 1.2: 2016-09-28
  Changes: Database references
• Version 1.3: 2020-02-26
  Changes: Data collection, Database references, Derived calculations