6IGK

Crystal Structure of human ETB receptor in complex with Endothelin-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 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 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

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endothelin receptor type B,Endolysin,Endothelin receptor type BA498Homo sapiensEnterobacteria phage RB59Mutation(s): 10 
Gene Names: EDNRBETRB
EC: 3.2.1.17
Find proteins for P24530 (Homo sapiens)
Explore P24530 
Go to UniProtKB:  P24530
NIH Common Fund Data Resources
PHAROS  P24530
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Endothelin-3B21Homo sapiensMutation(s): 0 
Gene Names: EDN3
Find proteins for P14138 (Homo sapiens)
Explore P14138 
Go to UniProtKB:  P14138
NIH Common Fund Data Resources
PHAROS  P14138
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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

Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.55α = 90
b = 172.28β = 90
c = 121.33γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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