6RZ9 | pdb_00006rz9

Crystal structure of the human cysteinyl leukotriene receptor 2 in complex with ONO-2770372

• PDB DOI: https://doi.org/10.2210/pdb6RZ9/pdb

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


• Deposited: 2019-06-12 Released: 2019-12-11 
• Deposition Author(s): Gusach, A., Luginina, A., Marin, E., Brouillette, R.L., Besserer-Offroy, E., Longpre, J.M., Ishchenko, A., Popov, P., Fujimoto, T., Maruyama, T., Stauch, B., Ergasheva, M., Romanovskaya, D., Stepko, A., Kovalev, K., Shevtsov, M., Gordeliy, V., Han, G.W., Sarret, P., Katritch, V., Borshchevskiy, V., Mishin, A., Cherezov, V.
• Funding Organization(s): Russian Science Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Canadian Institutes of Health Research, Fonds de Recherche du Quebec - Nature et Technologies

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 
  0.254 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.217 (Depositor) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Structural basis of ligand selectivity and disease mutations in cysteinyl leukotriene receptors.

Gusach, A., Luginina, A., Marin, E., Brouillette, R.L., Besserer-Offroy, E., Longpre, J.M., Ishchenko, A., Popov, P., Patel, N., Fujimoto, T., Maruyama, T., Stauch, B., Ergasheva, M., Romanovskaia, D., Stepko, A., Kovalev, K., Shevtsov, M., Gordeliy, V., Han, G.W., Katritch, V., Borshchevskiy, V., Sarret, P., Mishin, A., Cherezov, V.

(2019) Nat Commun 10: 5573-5573

• PubMed: 31811124 
• DOI: https://doi.org/10.1038/s41467-019-13348-2
• Primary Citation Related Structures: 
  6RZ6, 6RZ7, 6RZ8, 6RZ9


• PubMed Abstract: 
  

  Cysteinyl leukotriene G protein-coupled receptors CysLT ₁ and CysLT ₂ regulate pro-inflammatory responses associated with allergic disorders. While selective inhibition of CysLT ₁ R has been used for treating asthma and associated diseases for over two decades, CysLT ₂ R has recently started to emerge as a potential drug target against atopic asthma, brain injury and central nervous system disorders, as well as several types of cancer. Here, we describe four crystal structures of CysLT ₂ R in complex with three dual CysLT ₁ R/CysLT ₂ R antagonists. The reported structures together with the results of comprehensive mutagenesis and computer modeling studies shed light on molecular determinants of CysLTR ligand selectivity and specific effects of disease-related single nucleotide variants.

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Organizational Affiliation: 
• Research Сenter for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia, 141701.
Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada.
Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA.
Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.
Merck Research Laboratories, Merck & Co Inc., 770 Sumneytown Pike, West Point, PA, 19486, USA.
Center for Computational and Data Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Building 1, Moscow, Russia, 121205.
Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
Ono Pharmaceutical Co., Ltd., 3-1-1 Sakurai, Shimamoto, Mishima, Osaka, 618-8585, Japan.
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria.
Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Center Jülich, Jülich, Germany.
Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France.
JuStruct: Jülich Center for Structural Biology, Research Center Jülich, Jülich, Germany.
Institute of Crystallography, RWTH Aachen University, Aachen, Germany.
Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada. [e-mail].
Research Сenter for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia, 141701. [e-mail].
Research Сenter for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia, 141701. [e-mail].
Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA. [e-mail].
Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA. [e-mail].
Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.8 kDa 
• Atom Count: 3,106 
• Modeled Residue Count: 363 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteinyl leukotriene receptor 2,Soluble cytochrome b562,Cysteinyl leukotriene receptor 2	A	405	Homo sapiens, Escherichia coli	Mutation(s): 6  Gene Names: CYSLTR2, CYSLT2, CYSLT2R, PSEC0146, 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 Q9NS75 (Homo sapiens) Explore Q9NS75  Go to UniProtKB:  Q9NS75
PHAROS:  Q9NS75 GTEx:  ENSG00000152207
UniProt Groups	P0ABE7Q9NS75

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KO5 (Subject of Investigation/LOI)	B [auth A]	(2~{S})-8-[[4-[4-(5-fluoranyl-2-methyl-phenyl)butoxy]phenyl]carbonylamino]-4-(4-oxidanyl-4-oxidanylidene-butyl)-2,3-dih ydro-1,4-benzoxazine-2-carboxylic acid C31 H33 F N2 O7 AXUGAYNPVSAVSA-MHZLTWQESA-N
CLR	C [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA	R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
1PE	D [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free:  0.254 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.217 (Depositor) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.63	α = 90
b = 170.21	β = 90
c = 85.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-11 
Deposition Author(s): Gusach, A., Luginina, A., Marin, E., Brouillette, R.L., Besserer-Offroy, E., Longpre, J.M., Ishchenko, A., Popov, P., Fujimoto, T., Maruyama, T., Stauch, B., Ergasheva, M., Romanovskaya, D., Stepko, A., Kovalev, K., Shevtsov, M., Gordeliy, V., Han, G.W., Sarret, P., Katritch, V., Borshchevskiy, V., Mishin, A., Cherezov, V.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	16-14-10273
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM127086
Canadian Institutes of Health Research	Canada	--
Fonds de Recherche du Quebec - Nature et Technologies	Canada	--

Revision History  

• Version 1.0: 2019-12-11
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Database references
• Version 1.2: 2022-03-30
  Changes: Author supporting evidence, Database references, Derived calculations, Structure summary
• Version 1.3: 2024-01-24
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary