3V2Y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 th ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sphingosine 1-phosphate receptor 1, Lysozyme chimera (E.C.3.2.1.17)
A
520Homo sapiensEnterobacteria phage T4
This entity is chimeric
Gene Names: S1PR1 (CHEDG1, EDG1), E
EC: 3.2.1.17
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Sphingosine 1-phosphate receptor
Find proteins for P21453 (Homo sapiens)
Go to Gene View: S1PR1
Go to UniProtKB:  P21453
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ML5
Query on ML5

Download SDF File 
Download CCD File 
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 SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ML5Ki: 18 - 77 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 107.940α = 90.00
b = 69.700β = 90.00
c = 81.930γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Microdiffactiondata scaling
PHASERphasing
SCALAdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-03-14
    Type: Database references
  • Version 1.2: 2017-06-21
    Type: Data collection, Database references, Source and taxonomy, Structure summary