6LRY

Crystal structure of human endothelin ETB receptor in complex with sarafotoxin S6b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.270 

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Literature

Crystal structure of human endothelin ETBreceptor in complex with sarafotoxin S6b.

Izume, T.Miyauchi, H.Shihoya, W.Nureki, O.

(2020) Biochem.Biophys.Res.Commun. --: --

  • DOI: 10.1016/j.bbrc.2019.12.091

  • PubMed Abstract: 
  • Sarafotoxins (SRTXs) are endothelin-like peptides extracted from snake venom. SRTXs stimulate the endothelin ET <sub>A </sub> and ET <sub>B </sub> receptors and enhance vasoconstriction, followed by left ventricular dysfunction and bronchoconstrictio ...

    Sarafotoxins (SRTXs) are endothelin-like peptides extracted from snake venom. SRTXs stimulate the endothelin ET A and ET B receptors and enhance vasoconstriction, followed by left ventricular dysfunction and bronchoconstriction. SRTXs include four major isopeptides, S6a-d, with different subtype selectivities. Here, we report the crystal structure of the human ET B receptor in complex with the non-selective sarafotoxin S6b at 3.0 Å resolution. This structure reveals the similarities and differences between the binding modes of the endothelins and S6b. Moreover, molecular dynamics simulations based on the S6b-bound receptor provides structural insight into the subtype selectivity of the sarafotoxins. Our study clarifies the recognition mechanism of the endothelin-like peptide families.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan. Electronic address: nureki@bs.s.u-tokyo.ac.jp.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan. Electronic address: wtrshh9@gmail.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endothelin receptor type B,Endolysin,Endothelin receptor type B
A
504Homo sapiensEnterobacteria phage RB59
This entity is chimeric
Mutation(s): 10 
Gene Names: EDNRB (ETRB), e
EC: 3.2.1.17
Find proteins for P24530 (Homo sapiens)
Go to Gene View: EDNRB
Go to UniProtKB:  P24530
Find proteins for A0A097J809 (Enterobacteria phage RB59)
Go to UniProtKB:  A0A097J809
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sarafotoxin-B
B
21Atractaspis engaddensisMutation(s): 0 
Find proteins for P13208 (Atractaspis engaddensis)
Go to UniProtKB:  P13208
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.270 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.120α = 90.00
b = 82.280β = 90.00
c = 166.780γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan16H06294

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release