7C4S

Sphingosine-1-phosphate receptor 3 with a natural ligand.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Endogenous agonist-bound S1PR3 structure reveals determinants of G protein-subtype bias.

Maeda, S.Shiimura, Y.Asada, H.Hirata, K.Luo, F.Nango, E.Tanaka, N.Toyomoto, M.Inoue, A.Aoki, J.Iwata, S.Hagiwara, M.

(2021) Sci Adv 7

  • DOI: 10.1126/sciadv.abf5325
  • Primary Citation of Related Structures:  
    7C4S

  • PubMed Abstract: 
  • Sphingosine-1-phosphate (S1P) regulates numerous important physiological functions, including immune response and vascular integrity, via its cognate receptors (S1PR1 to S1PR5); however, it remains unclear how S1P activates S1PRs upon binding. Here, we determined the crystal structure of the active human S1PR3 in complex with its natural agonist S1P at 3 ...

    Sphingosine-1-phosphate (S1P) regulates numerous important physiological functions, including immune response and vascular integrity, via its cognate receptors (S1PR1 to S1PR5); however, it remains unclear how S1P activates S1PRs upon binding. Here, we determined the crystal structure of the active human S1PR3 in complex with its natural agonist S1P at 3.2-Å resolution. S1P exhibits an unbent conformation in the long tunnel, which penetrates through the receptor obliquely. Compared with the inactive S1PR1 structure, four residues surrounding the alkyl tail of S1P (the "quartet core") exhibit orchestrating rotamer changes that accommodate the moiety, thereby inducing an active conformation. In addition, we reveal that the quartet core determines G protein selectivity of S1PR3. These results offer insight into the structural basis of activation and biased signaling in G protein-coupled receptors and will help the design of biased ligands for optimized therapeutics.


    Organizational Affiliation

    Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody Fab fragment light chainD [auth K],
A [auth L]
214Mus musculusMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody Fab fragment heavy chainB [auth H],
E [auth J]
219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Sphingosine 1-phosphate receptor 3C [auth A],
F [auth B]
378Homo sapiensMutation(s): 1 
Gene Names: S1PR3EDG3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99500 (Homo sapiens)
Explore Q99500 
Go to UniProtKB:  Q99500
PHAROS:  Q99500
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99500
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S1P (Subject of Investigation/LOI)
Query on S1P

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B]
(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
C18 H38 N O5 P
DUYSYHSSBDVJSM-KRWOKUGFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.48α = 90
b = 247.08β = 97.37
c = 98.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanP19am0101070
Japan Agency for Medical Research and Development (AMED)JapanJP19am0101079
Japan Society for the Promotion of Science (JSPS)Japan19J22636
Japan Society for the Promotion of Science (JSPS)Japan18H02394
Japan Society for the Promotion of Science (JSPS)Japan19H05776
Japan Society for the Promotion of Science (JSPS)Japan19H05777
Japan Society for the Promotion of Science (JSPS)Japan15H05721

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references