6IGL

Crystal Structure of human ETB receptor in complex with IRL1620


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structures of human ETBreceptor provide mechanistic insight into receptor activation and partial activation.

Shihoya, W.Izume, T.Inoue, A.Yamashita, K.Kadji, F.M.N.Hirata, K.Aoki, J.Nishizawa, T.Nureki, O.

(2018) Nat Commun 9: 4711-4711

  • DOI: 10.1038/s41467-018-07094-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Endothelin receptors (ET <sub>A </sub> and ET <sub>B </sub>) are class A GPCRs activated by vasoactive peptide endothelins, and are involved in blood pressure regulation. ET <sub>B </sub>-selective signalling induces vasorelaxation, and thus selectiv ...

    Endothelin receptors (ET A and ET B ) are class A GPCRs activated by vasoactive peptide endothelins, and are involved in blood pressure regulation. ET B -selective signalling induces vasorelaxation, and thus selective ET B agonists are expected to be utilized for improved anti-tumour drug delivery and neuroprotection. Here, we report the crystal structures of human ET B receptor in complex with ET B -selective agonist, endothelin-3 and an ET B -selective endothelin analogue IRL1620. The structure of the endothelin-3-bound receptor reveals that the disruption of water-mediated interactions between W6.48 and D2.50 is critical for receptor activation, while these hydrogen-bonding interactions are partially preserved in the IRL1620-bound structure. Consistently, functional analysis reveals the partial agonistic effect of IRL1620. The current findings clarify the detailed molecular mechanism for the coupling between the orthosteric pocket and the G-protein binding, and the partial agonistic effect of IRL1620, thus paving the way for the design of improved agonistic drugs targeting ET B .


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.,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. t-2438@bs.s.u-tokyo.ac.jp.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan. nureki@bs.s.u-tokyo.ac.jp.,RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.,Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Tokyo, 100-0004, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endothelin receptor type B,Endolysin,Endothelin receptor type B
A
498Homo sapiensMutation(s): 10 
Gene Names: EDNRB (ETRB)
Find proteins for P24530 (Homo sapiens)
Go to Gene View: EDNRB
Go to UniProtKB:  P24530
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IRL1620
B
15N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SIN
Query on SIN
B
NON-POLYMERC4 H6 O4

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 99.980α = 90.00
b = 303.860β = 90.00
c = 60.160γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan--

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release