Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 59.54 kDa 
• Atom Count: 3523 
• Modelled Residue Count: 455 
• Deposited Residue Count: 520 
• Unique protein chains: 1

3V2Y

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

• PDB DOI: 10.2210/pdb3V2Y/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Escherichia virus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


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

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, 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingosine 1-phosphate receptor 1, Lysozyme chimera (E.C.3.2.1.17)	A	520	Homo sapiens, Escherichia virus T4	Mutation(s): 2  Gene Names: S1PR1, CHEDG1, EDG1, E EC: 3.2.1.17 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P21453 (Homo sapiens) Explore P21453  Go to UniProtKB:  P21453
PHAROS:  P21453
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
UniProt Groups	P21453P00720

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ML5	B [auth A]	{(3R)-3-amino-4-[(3-hexylphenyl)amino]-4-oxobutyl}phosphonic acid C16 H27 N2 O4 P FWJRVGZWNDOOFH-OAHLLOKOSA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ML5	BindingDB:  3V2Y	Ki: min: 18, max: 77 (nM) from 2 assay(s)

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 = 107.94	α = 90
b = 69.7	β = 90
c = 81.93	γ = 90

Software Package:

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

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
  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