6RZ5

XFEL crystal structure of the human cysteinyl leukotriene receptor 1 in complex with zafirlukast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs.

Luginina, A.Gusach, A.Marin, E.Mishin, A.Brouillette, R.Popov, P.Shiriaeva, A.Besserer-Offroy, E.Longpre, J.M.Lyapina, E.Ishchenko, A.Patel, N.Polovinkin, V.Safronova, N.Bogorodskiy, A.Edelweiss, E.Hu, H.Weierstall, U.Liu, W.Batyuk, A.Gordeliy, V.Han, G.W.Sarret, P.Katritch, V.Borshchevskiy, V.Cherezov, V.

(2019) Sci Adv 5: eaax2518-eaax2518

  • DOI: 10.1126/sciadv.aax2518
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The G protein-coupled cysteinyl leukotriene receptor CysLT <sub>1 </sub>R mediates inflammatory processes and plays a major role in numerous disorders, including asthma, allergic rhinitis, cardiovascular disease, and cancer. Selective CysLT <sub>1 </ ...

    The G protein-coupled cysteinyl leukotriene receptor CysLT 1 R mediates inflammatory processes and plays a major role in numerous disorders, including asthma, allergic rhinitis, cardiovascular disease, and cancer. Selective CysLT 1 R antagonists are widely prescribed as antiasthmatic drugs; however, these drugs demonstrate low effectiveness in some patients and exhibit a variety of side effects. To gain deeper understanding into the functional mechanisms of CysLTRs, we determined the crystal structures of CysLT 1 R bound to two chemically distinct antagonists, zafirlukast and pranlukast. The structures reveal unique ligand-binding modes and signaling mechanisms, including lateral ligand access to the orthosteric pocket between transmembrane helices TM4 and TM5, an atypical pattern of microswitches, and a distinct four-residue-coordinated sodium site. These results provide important insights and structural templates for rational discovery of safer and more effective drugs.


    Organizational Affiliation

    Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.,Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia.,Department of Physics, Arizona State University, Tempe, AZ 85287, USA.,Juelich Center for Structural Biology, Research Center Juelich, Juelich, Germany.,Institute of Crystallography, RWTH Aachen University, Aachen, Germany.,Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble 38000, France.,ELI Beamlines, Institute of Physics, Czech Academy of Sciences, 18221 Prague, Czech Republic.,Departments of Chemistry and Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,Institute of Complex Systems, ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1
A, B
423Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: cybC, CYSLTR1 (CYSLT1)
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for Q9Y271 (Homo sapiens)
Go to Gene View: CYSLTR1
Go to UniProtKB:  Q9Y271
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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Download CCD File 
A, B
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
OLA
Query on OLA

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Download CCD File 
A, B
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
ZLK
Query on ZLK

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Download CCD File 
A, B
zafirlukast
C31 H33 N3 O6 S
YEEZWCHGZNKEEK-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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Download CCD File 
A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.590α = 76.31
b = 68.580β = 76.68
c = 87.390γ = 81.21
Software Package:
Software NamePurpose
CrystFELdata scaling
PHASERphasing
BUSTERrefinement
CrystFELdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation16-14-10273
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35 GM127086
Canadian Institutes of Health ResearchCanadaFDN-148413

Revision History 

  • Version 1.0: 2019-10-30
    Type: Initial release