6K1Q

Human endothelin receptor type-B in complex with inverse agonist IRL2500


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report



Literature

Crystal structure of human endothelin ETBreceptor in complex with peptide inverse agonist IRL2500.

Nagiri, C.Shihoya, W.Inoue, A.Kadji, F.M.N.Aoki, J.Nureki, O.

(2019) Commun Biol 2: 236-236

  • DOI: 10.1038/s42003-019-0482-7
  • Primary Citation of Related Structures:  
    6K1Q

  • PubMed Abstract: 
  • Endothelin receptors (ET A and ET B ) are G-protein-coupled receptors activated by endothelin-1 and are involved in blood pressure regulation. IRL2500 is a peptide-mimetic of the C-terminal tripeptide of endothelin-1, and has b ...

    Endothelin receptors (ET A and ET B ) are G-protein-coupled receptors activated by endothelin-1 and are involved in blood pressure regulation. IRL2500 is a peptide-mimetic of the C-terminal tripeptide of endothelin-1, and has been characterized as a potent ET B -selective antagonist, which has preventive effects against brain edema. Here, we report the crystal structure of the human ET B receptor in complex with IRL2500 at 2.7 Å-resolution. The structure revealed the different binding modes between IRL2500 and endothelin-1, and provides structural insights into its ET B -selectivity. Notably, the biphenyl group of IRL2500 penetrates into the transmembrane core proximal to D 2.50 , thus stabilizing the inactive conformation. Using the newly-established constitutively active mutant, we clearly demonstrate that IRL2500 functions as an inverse agonist for the ET B receptor. The current findings will expand the chemical space of ETR antagonists and facilitate the design of inverse agonists for other class A GPCRs.


    Organizational Affiliation

    1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endothelin B receptor,Endolysin,Endothelin B receptorA464Homo sapiensEscherichia virus T4Mutation(s): 9 
Gene Names: EDNRBETRB
EC: 3.2.1.17
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
endothelin ETB receptor with bound IRL2500
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P24530 (Homo sapiens)
Explore P24530 
Go to UniProtKB:  P24530
NIH Common Fund Data Resources
PHAROS  P24530
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D2U
Query on D2U

Download CCD File 
A
(2~{S})-2-[[(2~{R})-2-[(3,5-dimethylphenyl)carbonyl-methyl-amino]-3-(4-phenylphenyl)propanoyl]amino]-3-(1~{H}-indol-3-yl)propanoic acid
C36 H35 N3 O4
UZDORQWMYRRLQV-JHOUSYSJSA-N
 Ligand Interaction
OLC
Query on OLC

Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.91α = 90
b = 109.91β = 90
c = 291.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16H06294

Revision History 

  • Version 1.0: 2019-07-17
    Type: Initial release