6IGL

Crystal Structure of human ETB receptor in complex with IRL1620


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

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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:  
    6IGK, 6IGL

  • 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 selective ET B agonists are expected to be utilized for improved anti-tumour drug delivery and neuroprotection ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endothelin receptor type B,Endolysin,Endothelin receptor type BA498Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24530
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IRL1620B15Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.98α = 90
b = 303.86β = 90
c = 60.16γ = 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--

Revision History  (Full details and data files)

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