Crystal Structure of a Lipid G protein-Coupled Receptor at 2.80A

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Crystal structure of a lipid G protein-coupled receptor.

Hanson, M.A.Roth, C.B.Jo, E.Griffith, M.T.Scott, F.L.Reinhart, G.Desale, H.Clemons, B.Cahalan, S.M.Schuerer, S.C.Sanna, M.G.Han, G.W.Kuhn, P.Rosen, H.Stevens, R.C.

(2012) Science 335: 851-855

  • DOI: https://doi.org/10.1126/science.1215904
  • Primary Citation of Related Structures:  
    3V2W, 3V2Y

  • PubMed Abstract: 

    The lyso-phospholipid sphingosine 1-phosphate modulates lymphocyte trafficking, endothelial development and integrity, heart rate, and vascular tone and maturation by activating G protein-coupled sphingosine 1-phosphate receptors. Here, we present the crystal structure of the sphingosine 1-phosphate receptor 1 fused to T4-lysozyme (S1P(1)-T4L) in complex with an antagonist sphingolipid mimic. Extracellular access to the binding pocket is occluded by the amino terminus and extracellular loops of the receptor. Access is gained by ligands entering laterally between helices I and VII within the transmembrane region of the receptor. This structure, along with mutagenesis, agonist structure-activity relationship data, and modeling, provides a detailed view of the molecular recognition and requirement for hydrophobic volume that activates S1P(1), resulting in the modulation of immune and stromal cell responses.

  • Organizational Affiliation

    Receptos, 10835 Road to the Cure, San Diego, CA 92121, USA. mhanson@receptos.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sphingosine 1-phosphate receptor 1, Lysozyme chimera (E.C. sapiensTequatrovirus T4Mutation(s): 2 
Gene Names: S1PR1CHEDG1EDG1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P21453 (Homo sapiens)
Explore P21453 
Go to UniProtKB:  P21453
PHAROS:  P21453
GTEx:  ENSG00000170989 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P21453
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ML5

Download Ideal Coordinates CCD File 
B [auth A]{(3R)-3-amino-4-[(3-hexylphenyl)amino]-4-oxobutyl}phosphonic acid
C16 H27 N2 O4 P
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
Binding Affinity Annotations 
IDSourceBinding Affinity
ML5 BindingDB:  3V2Y Ki: min: 18, max: 77 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.94α = 90
b = 69.7β = 90
c = 81.93γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Microdiffactiondata scaling
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-03-14
    Changes: Database references
  • Version 1.2: 2017-06-21
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Refinement description, Structure summary