6LRY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 

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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 528: 383-388

  • DOI: 10.1016/j.bbrc.2019.12.091
  • Primary Citation of Related Structures:  
    6LRY

  • PubMed Abstract: 
  • 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 ...

    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. Electronic address: nureki@bs.s.u-tokyo.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endothelin receptor type B,Endolysin,Endothelin receptor type BA504Homo sapiensEnterobacteria phage RB59Mutation(s): 10 
Gene Names: EDNRBETRBeRB59_126
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P24530 (Homo sapiens)
Explore P24530 
Go to UniProtKB:  P24530
PHAROS:  P24530
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sarafotoxin-BB21Atractaspis engaddensisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13208 (Atractaspis engaddensis)
Explore P13208 
Go to UniProtKB:  P13208
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.12α = 90
b = 82.28β = 90
c = 166.78γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

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  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references