3V2Y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.3 of the entry. See complete history


Literature

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: 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sphingosine 1-phosphate receptor 1, Lysozyme chimera (E.C.3.2.1.17)A520Homo sapiensEscherichia virus T4Mutation(s): 2 
Gene Names: S1PR1CHEDG1EDG1E
EC: 3.2.1.17
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors: Class A
Protein: 
Sphingosine 1-phosphate receptor
Find proteins for P21453 (Homo sapiens)
Explore P21453 
Go to UniProtKB:  P21453
NIH Common Fund Data Resources
PHAROS:  P21453
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ML5
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
FWJRVGZWNDOOFH-OAHLLOKOSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ML5Ki:  18   nM  BindingDB
ML5Ki:  77   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
BUSTERrefinement
XDSdata reduction
Microdiffactiondata scaling
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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