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- PDB-6rz5: XFEL crystal structure of the human cysteinyl leukotriene recepto... -

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Basic information

Entry
Database: PDB / ID: 6rz5
TitleXFEL crystal structure of the human cysteinyl leukotriene receptor 1 in complex with zafirlukast
ComponentsCysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1
KeywordsMEMBRANE PROTEIN / GPCR / LCP / cysteinyl leukotriene / LTD4 / cyslt1 / cysltr1 / cyslt1r / asthma / zafirlukast / BRIL / sodium site / Cysteinyl Leukotriene Receptor 1 / XFEL / Serial Femtosecond Crystallography / SFX
Function / homology
Function and homology information


cysteinyl leukotriene receptor activity / leukotriene receptor activity / Leukotriene receptors / LTC4-CYSLTR mediated IL4 production / respiratory gaseous exchange by respiratory system / G protein-coupled peptide receptor activity / inflammatory response to antigenic stimulus / neuropeptide signaling pathway / establishment of localization in cell / electron transport chain ...cysteinyl leukotriene receptor activity / leukotriene receptor activity / Leukotriene receptors / LTC4-CYSLTR mediated IL4 production / respiratory gaseous exchange by respiratory system / G protein-coupled peptide receptor activity / inflammatory response to antigenic stimulus / neuropeptide signaling pathway / establishment of localization in cell / electron transport chain / defense response / chemotaxis / calcium ion transport / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / Potential therapeutics for SARS / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / iron ion binding / heme binding / membrane / plasma membrane
Similarity search - Function
Cysteinyl leukotriene receptor 1 / Cysteinyl leukotriene receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / zafirlukast / Soluble cytochrome b562 / Cysteinyl leukotriene receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsLuginina, A. / Gusach, A. / Marin, E. / Mishin, A. / Brouillette, R. / Popov, P. / Shiryaeva, A. / Besserer-Offroy, E. / Longpre, J.M. / Lyapina, E. ...Luginina, A. / Gusach, A. / Marin, E. / Mishin, A. / Brouillette, R. / Popov, P. / Shiryaeva, A. / Besserer-Offroy, E. / Longpre, J.M. / Lyapina, E. / Ishchenko, A. / Patel, N. / Polovinkin, V. / Safronova, N. / Bogorodskiy, A. / Edelweiss, E. / Liu, W. / Batyuk, A. / Gordeliy, V. / Han, G.W. / Sarret, P. / Katritch, V. / Borshchevskiy, V. / Cherezov, V.
Funding support Russian Federation, United States, Canada, 3items
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 ResearchFDN-148413 Canada
CitationJournal: Sci Adv / Year: 2019
Title: Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs.
Authors: 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, ...Authors: 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.
History
DepositionJun 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 2.0Jan 15, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _entity_src_gen.host_org_common_name / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num
Revision 3.0Apr 8, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num
Revision 3.1Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 3.2Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Revision 3.3Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1
B: Cysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,29344
Polymers95,8542
Non-polymers13,43942
Water18010
1
A: Cysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,72323
Polymers47,9271
Non-polymers6,79622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,57021
Polymers47,9271
Non-polymers6,64320
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.590, 68.580, 87.390
Angle α, β, γ (deg.)76.31, 76.68, 81.21
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1 / CysLTR1 / Cysteinyl leukotriene D4 receptor / LTD4 receptor / G-protein coupled receptor HG55 / ...CysLTR1 / Cysteinyl leukotriene D4 receptor / LTD4 receptor / G-protein coupled receptor HG55 / HMTMF81 / Cytochrome b-562 / CysLTR1 / Cysteinyl leukotriene D4 receptor / LTD4 receptor / G-protein coupled receptor HG55 / HMTMF81


Mass: 47927.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: CYSLTR1, CYSLT1, cybC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y271, UniProt: P0ABE7

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Non-polymers , 6 types, 52 molecules

#2: Chemical ChemComp-ZLK / zafirlukast


Mass: 575.675 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H33N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 75-175 mM sodium phosphate 24-34% v/v PEG400 100 mM HEPES pH 7.0 1 uM zafirlukast

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.302 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Aug 21, 2016 / Details: pair of Kirkpatrick-Baez mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.302 Å / Relative weight: 1
ReflectionResolution: 2.53→20 Å / Num. obs: 30258 / % possible obs: 100 % / Redundancy: 82.7 % / Biso Wilson estimate: 65.2 Å2 / CC1/2: 0.98 / R split: 0.2 / Net I/σ(I): 3.2
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 43.2 % / Num. unique obs: 2988 / CC1/2: 0.2 / R split: 2.19 / % possible all: 100
Serial crystallography measurementFocal spot size: 2.25 µm2 / Pulse duration: 43 fsec. / Pulse photon energy: 9.52 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryDescription: LCP jet / Method: injection
Serial crystallography sample delivery injectionDescription: LCP jet / Flow rate: 0.2 µL/min / Injector diameter: 50 µm
Serial crystallography data reductionCrystal hits: 40720 / Frames indexed: 30129 / Frames total: 315374 / Lattices indexed: 32568 / XFEL pulse events: 315374

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
CrystFEL0.6.3+23ea03c7data reduction
CrystFEL0.6.3+23ea03c7data scaling
PHASER1.12-2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RZ4

6rz4


Resolution: 2.53→19.84 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.415 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.255
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1508 5 %RANDOM
Rwork0.189 ---
obs0.191 30186 99.7 %-
Displacement parametersBiso mean: 92.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.0892 Å21.1108 Å22.9794 Å2
2--7.8357 Å20.1126 Å2
3----7.7465 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.53→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5527 0 572 10 6109
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016237HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.088375HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2082SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1005HARMONIC5
X-RAY DIFFRACTIONt_it6237HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion20.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion819SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6750SEMIHARMONIC4
LS refinement shellResolution: 2.53→2.55 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2633 -4.97 %
Rwork0.2197 574 -
all0.2219 604 -
obs--98.4 %
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)
11.04260.1658-0.3138-0.0354-0.1050.9688-0.0252-0.11980.1251-0.0266-0.0586-0.0437-0.0736-0.02780.0838-0.28660.0186-0.0239-0.3093-0.0601-0.21072.129615.55751.6921
20.4985-0.06050.61210.5089-0.4540.5653-0.0476-0.0031-0.27870.09980.01750.1323-0.17060.02250.0301-0.29140.034-0.0102-0.31420.0185-0.1065-2.1224-15.75524.1544
31.06890.81830.56912.563-0.4098-0.04740.0091-0.2408-0.05710.1246-0.05890.2615-0.125-0.0880.0499-0.30130.0644-0.0321-0.224-0.0698-0.1556-1.4664-0.6662-6.3049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ L|* }

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