Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction | Predict Membrane 

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.66 kDa 
• Atom Count: 3073 
• Modelled Residue Count: 382 
• Deposited Residue Count: 459 
• Unique protein chains: 1

4Z36

Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO-3080573

• DOI: 10.2210/pdb4Z36/pdb

• Classification: TRANSPORT PROTEIN/inhibitor
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2015-03-30 Released: 2015-06-03 
• Deposition Author(s): Chrencik, J.E., Roth, C.B., Terakado, M., Kurata, H., Omi, R., Kihara, Y., Warshaviak, D., Nakade, S., Asmar-Rovira, G., Mileni, M., Mizuno, H., Griffith, M.T., Rodgers, C., Han, G.W., Velasquez, J., Chun, J., Stevens, R.C., Hanson, M.A., GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.292 
• R-Value Work: 0.272 
• R-Value Observed: 0.273 

Literature

Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1.

Chrencik, J.E., Roth, C.B., Terakado, M., Kurata, H., Omi, R., Kihara, Y., Warshaviak, D., Nakade, S., Asmar-Rovira, G., Mileni, M., Mizuno, H., Griffith, M.T., Rodgers, C., Han, G.W., Velasquez, J., Chun, J., Stevens, R.C., Hanson, M.A.

(2015) Cell 161: 1633-1643

• PubMed: 26091040 
• DOI: 10.1016/j.cell.2015.06.002
• Primary Citation of Related Structures:  
  4Z35, 4Z36, 4Z34


• PubMed Abstract: 
  

Lipid biology continues to emerge as an area of significant therapeutic interest, particularly as the result of an enhanced understanding of the wealth of signaling molecules with diverse physiological properties. This growth in knowledge is epitomized by lysophosphatidic acid (LPA), which functions through interactions with at least six cognate G protein-coupled receptors. Herein, we present three crystal structures of LPA1 in complex with antagonist tool compounds selected and designed through structural and stability analyses. Structural analysis combined with molecular dynamics identified a basis for ligand access to the LPA1 binding pocket from the extracellular space contrasting with the proposed access for the sphingosine 1-phosphate receptor. Characteristics of the LPA1 binding pocket raise the possibility of promiscuous ligand recognition of phosphorylated endocannabinoids. Cell-based assays confirmed this hypothesis, linking the distinct receptor systems through metabolically related ligands with potential functional and therapeutic implications for treatment of disease.

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Organizational Affiliation: 

Department of Structural Discovery, Receptos, San Diego, CA 92121, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysophosphatidic acid receptor 1,Soluble cytochrome b562	A	459	Homo sapiens, Escherichia coli	Mutation(s): 3  Gene Names: LPAR1, EDG2, LPA1, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for Q92633 (Homo sapiens) Explore Q92633  Go to UniProtKB:  Q92633
PHAROS:  Q92633 GTEx:  ENSG00000198121

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ON3	B [auth A]	1-(4-{[(2S,3R)-2-(2,3-dihydro-1H-inden-2-yloxy)-3-(3,5-dimethoxy-4-methylphenyl)-3-hydroxypropyl]oxy}phenyl)cyclopropan ecarboxylic acid C31 H34 O7 FVESDCZDESZGHA-URLMMPGGSA-N
1WV	C [auth A]	(2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate C17 H32 O4 LVBAGTJIDOCNIJ-INIZCTEOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.292 
• R-Value Work: 0.272 
• R-Value Observed: 0.273 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.35	α = 90
b = 111.93	β = 90
c = 153.96	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-03-30 
• Released Date: 2015-06-03 
Deposition Author(s): Chrencik, J.E., Roth, C.B., Terakado, M., Kurata, H., Omi, R., Kihara, Y., Warshaviak, D., Nakade, S., Asmar-Rovira, G., Mileni, M., Mizuno, H., Griffith, M.T., Rodgers, C., Han, G.W., Velasquez, J., Chun, J., Stevens, R.C., Hanson, M.A., GPCR Network (GPCR)

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2015-07-01
  Changes: Database references