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- PDB-6rz8: Crystal structure of the human cysteinyl leukotriene receptor 2 i... -

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Basic information

Entry
Database: PDB / ID: 6rz8
TitleCrystal structure of the human cysteinyl leukotriene receptor 2 in complex with ONO-2080365
ComponentsCysteinyl leukotriene receptor 2,Soluble cytochrome b562,Cysteinyl leukotriene receptor 2
KeywordsMEMBRANE PROTEIN / GPCR / LCP / cysteinyl leukotriene / cyslt2 / cysltr2 / cyslt2r / asthma / BRIL / Cysteinyl Leukotriene Receptor 2
Function / homology
Function and homology information


cysteinyl leukotriene receptor activity / leukotriene receptor activity / Leukotriene receptors / LTC4-CYSLTR mediated IL4 production / G protein-coupled peptide receptor activity / neuropeptide signaling pathway / electron transport chain / G alpha (s) signalling events / G alpha (q) signalling events / periplasmic space ...cysteinyl leukotriene receptor activity / leukotriene receptor activity / Leukotriene receptors / LTC4-CYSLTR mediated IL4 production / G protein-coupled peptide receptor activity / neuropeptide signaling pathway / electron transport chain / G alpha (s) signalling events / G alpha (q) signalling events / periplasmic space / electron transfer activity / immune response / iron ion binding / heme binding / plasma membrane
Similarity search - Function
Cysteinyl leukotriene receptor 2 / Cysteinyl leukotriene receptor / Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. ...Cysteinyl leukotriene receptor 2 / Cysteinyl leukotriene receptor / Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KNZ / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / Cysteinyl leukotriene receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGusach, A. / Luginina, A. / Marin, E. / Brouillette, R.L. / Besserer-Offroy, E. / Longpre, J.M. / Ishchenko, A. / Popov, P. / Fujimoto, T. / Maruyama, T. ...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 support Russian Federation, United States, Canada, 4items
OrganizationGrant numberCountry
Russian Science Foundation16-14-10273 Russian Federation
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127086 United States
Canadian Institutes of Health Research Canada
Fonds de Recherche du Quebec - Nature et Technologies Canada
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of ligand selectivity and disease mutations in cysteinyl leukotriene receptors.
Authors: 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. / ...Authors: 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.
History
DepositionJun 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_audit_support / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteinyl leukotriene receptor 2,Soluble cytochrome b562,Cysteinyl leukotriene receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,01115
Polymers45,9961
Non-polymers5,01514
Water30617
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: BIOLOGICAL UNIT IS UNKNOWN
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint11 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.440, 78.440, 172.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Cysteinyl leukotriene receptor 2,Soluble cytochrome b562,Cysteinyl leukotriene receptor 2 / CysLTR2 / G-protein coupled receptor GPCR21 / hGPCR21 / G-protein coupled receptor HG57 / HPN321 / ...CysLTR2 / G-protein coupled receptor GPCR21 / hGPCR21 / G-protein coupled receptor HG57 / HPN321 / Cytochrome b-562 / CysLTR2 / G-protein coupled receptor GPCR21 / hGPCR21 / G-protein coupled receptor HG57 / HPN321


Mass: 45995.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: CYSLTR2, CYSLT2, CYSLT2R, PSEC0146, cybC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NS75, UniProt: P0ABE7
#2: Chemical ChemComp-KNZ / (2~{S})-8-[[4-[4-[2,3-bis(fluoranyl)phenoxy]butoxy]-2-fluoranyl-phenyl]carbonylamino]-4-(4-oxidanyl-4-oxidanylidene-but yl)-2,3-dihydro-1,4-benzoxazine-2-carboxylic acid / ONO-2080365


Mass: 602.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H29F3N2O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 100 mM K Formate 30% v/v PEG400 100 mM TRIS-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 14227 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.99 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.066 / Net I/σ(I): 9.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 13.8 % / Rmerge(I) obs: 2.758 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.41 / Rpim(I) all: 0.766 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
BUSTER2.10.3refinement
XDS20161205data reduction
XSCALE20180319data scaling
PHASER1.12-2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RZ4

6rz4


Resolution: 2.7→29.924 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.04
RfactorNum. reflection% reflection
Rfree0.2465 711 5 %
Rwork0.1938 --
obs0.1964 14226 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 82.2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 222 17 3003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043032
X-RAY DIFFRACTIONf_angle_d0.7484078
X-RAY DIFFRACTIONf_dihedral_angle_d11.5931799
X-RAY DIFFRACTIONf_chiral_restr0.048482
X-RAY DIFFRACTIONf_plane_restr0.005494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.90840.3451370.26942688X-RAY DIFFRACTION100
2.9084-3.20080.33871350.24442706X-RAY DIFFRACTION100
3.2008-3.66330.24961470.20382687X-RAY DIFFRACTION100
3.6633-4.61260.23291400.1582724X-RAY DIFFRACTION100
4.6126-29.9260.21431520.18982712X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.37570.1641-0.05752.19181.15482.146-0.0145-0.05510.13320.0673-0.07770.2397-0.1369-0.08280.03070.38510.02830.02660.2620.02690.4058109.979964.5101-6.767
27.5364-1.6287-0.05457.95082.95543.65190.49150.00410.0511-0.4216-0.21950.01361.6273-1.0023-0.28031.08960.0152-0.11070.87180.05680.5252130.56453.248739.5294
34.5140.3309-0.70123.68890.62524.62120.2431-0.4049-0.06650.2641-0.16140.11320.07510.4488-0.04820.3073-0.0303-0.05330.3360.01880.4799118.461758.1606-6.7567
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 31 through 232)
2X-RAY DIFFRACTION2(chain 'A' and resid 1001 through 1106)
3X-RAY DIFFRACTION3(chain 'A' and resid 240 through 313)

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