Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59536.75 
• Atom Count: 3512 
• Residue Count: 520 
• Unique protein chains: 1

3V2Y

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

• DOI: 10.2210/pdb3V2Y/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Enterobacteria phage T4
• Expression System: Spodoptera frugiperda
• Mutation(s): 2 


• Deposited: 2011-12-12 Released: 2012-02-15 
• Deposition Author(s): 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., GPCR Network (GPCR)

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Experimental Data Snapshot

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

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

• PubMed: 22344443 
• 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 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.

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Organizational Affiliation: 

Receptos, 10835 Road to the Cure, San Diego, CA 92121, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Sphingosine 1-phosphate receptor 1, Lysozyme chimera (E.C.3.2.1.17)	A	520	Homo sapiens, Enterobacteria phage T4 This entity is chimeric	Mutation(s): 2  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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ML5	A	{(3R)-3-amino-4-[(3-hexylphenyl)amino]-4-oxobutyl}phosphonic acid C16 H27 N2 O4 P FWJRVGZWNDOOFH-OAHLLOKOSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ML5	Ki: 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 = 107.940	α = 90.00
b = 69.700	β = 90.00
c = 81.930	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
Microdiffaction	data scaling
PHASER	phasing
SCALA	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-12 
• Released Date: 2012-02-15 
• Deposition Author(s): 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., GPCR Network (GPCR)

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