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- PDB-6rz4: Crystal structure of cysteinyl leukotriene receptor 1 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6rz4
TitleCrystal structure of cysteinyl leukotriene receptor 1 in complex with pranlukast
ComponentsCysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1
KeywordsMEMBRANE PROTEIN / GPCR / LCP / cysteinyl leukotriene / LTD4 / cyslt1 / cysltr1 / cyslt1r asthma / pranlukast / BRIL / sodium site / Cysteinyl Leukotriene Receptor 1
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 / inflammatory response to antigenic stimulus / G protein-coupled peptide receptor activity / neuropeptide signaling pathway / positive regulation of glial cell proliferation / positive regulation of vasoconstriction ...cysteinyl leukotriene receptor activity / leukotriene receptor activity / Leukotriene receptors / LTC4-CYSLTR mediated IL4 production / respiratory gaseous exchange by respiratory system / inflammatory response to antigenic stimulus / G protein-coupled peptide receptor activity / neuropeptide signaling pathway / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / establishment of localization in cell / electron transport chain / defense response / positive regulation of angiogenesis / chemotaxis / calcium ion transport / positive regulation of cytosolic calcium ion concentration / cellular response to hypoxia / 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 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 1 / 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
pranlukast / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / Cysteinyl leukotriene receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / entity_src_gen ...atom_site / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_torsion / struct_conf / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_seq_id / _entity_src_gen.host_org_common_name ..._atom_site.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_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 / Database references / Derived calculations / Structure summary
Category: atom_site / pdbx_poly_seq_scheme ...atom_site / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref_seq
Item: _atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num ..._atom_site.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 / _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_end
Revision 3.1Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 3.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 3.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,92313
Polymers47,9271
Non-polymers3,99612
Water28816
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: BIOLOGICAL UNIT IS UNKNOWN
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-8 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.630, 45.350, 86.430
Angle α, β, γ (deg.)90.00, 91.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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.: 1
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 , 5 types, 28 molecules

#2: Chemical ChemComp-KNT / pranlukast


Mass: 481.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H23N5O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C21H40O4
#5: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.41 Å3/Da / Density % sol: 49 % / Description: crystals had a twiggy shape
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 100 mM sodium citrate pH 6 200-600 mM lithium nitrate 30-38% v/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 12749 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 39.62 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.269 / Net I/σ(I): 7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 8 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1278 / CC1/2: 0.642 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS20161101data reduction
XSCALE20161101data scaling
PHASER1.12-2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XNW,4EIY

4xnw

4eiy


Resolution: 2.7→29.3 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.832 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 2.308 / SU Rfree Blow DPI: 0.333
RfactorNum. reflection% reflectionSelection details
Rfree0.254 641 5.03 %RANDOM
Rwork0.228 ---
obs0.229 12755 99.9 %-
Displacement parametersBiso mean: 65.03 Å2
Baniso -1Baniso -2Baniso -3
1-2.6949 Å20 Å215.8184 Å2
2---6.4543 Å20 Å2
3---3.7594 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 170 16 3185
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083258HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.894401HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1088SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes567HARMONIC5
X-RAY DIFFRACTIONt_it3258HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.69
X-RAY DIFFRACTIONt_other_torsion20.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion435SEMIHARMONIC5
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_contact3773SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.96 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2532 152 5.03 %
Rwork0.2513 2868 -
all0.2514 3020 -
obs--99.97 %

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