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- PDB-4z35: Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in co... -

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Basic information

Entry
Database: PDB / ID: 4z35
TitleCrystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO-9910539
ComponentsLysophosphatidic acid receptor 1,Soluble cytochrome b562
KeywordsTRANSPORT PROTEIN/inhibitor / human lysophosphatidic acid receptor 1 (LPA1) / G-protein coupled receptor (GPCR) / membrane protein / antagonist / endogenous ligand / PSI-biology / structural genomics / GPCR network / lipidic cubic phase (LCP) / compound design / polypharmacology / lipid receptor / TRANSPORT PROTEIN-inhibitor complex
Function / homology
Function and homology information


cellular response to 1-oleoyl-sn-glycerol 3-phosphate / lysophosphatidic acid receptor activity / positive regulation of smooth muscle cell chemotaxis / Lysosphingolipid and LPA receptors / : / lysophosphatidic acid binding / negative regulation of cilium assembly / regulation of synaptic vesicle cycle / corpus callosum development / bleb assembly ...cellular response to 1-oleoyl-sn-glycerol 3-phosphate / lysophosphatidic acid receptor activity / positive regulation of smooth muscle cell chemotaxis / Lysosphingolipid and LPA receptors / : / lysophosphatidic acid binding / negative regulation of cilium assembly / regulation of synaptic vesicle cycle / corpus callosum development / bleb assembly / negative regulation of cAMP-mediated signaling / oligodendrocyte development / cellular response to oxygen levels / regulation of metabolic process / regulation of postsynaptic neurotransmitter receptor internalization / optic nerve development / positive regulation of Rho protein signal transduction / positive regulation of dendritic spine development / G-protein alpha-subunit binding / GABA-ergic synapse / positive regulation of stress fiber assembly / myelination / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cerebellum development / cell chemotaxis / neurogenesis / dendritic shaft / PDZ domain binding / G protein-coupled receptor activity / electron transport chain / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of neuron projection development / presynaptic membrane / regulation of cell shape / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (q) signalling events / postsynaptic membrane / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / dendritic spine / periplasmic space / electron transfer activity / endosome / iron ion binding / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / neuronal cell body / glutamatergic synapse / heme binding / cell surface / plasma membrane / cytoplasm
Similarity search - Function
Lysophosphatidic acid receptor EDG-2 / Lysophosphatidic acid receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 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
(2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate / Chem-ON9 / Soluble cytochrome b562 / Lysophosphatidic acid receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChrencik, J.E. / Roth, C.B. / Terakado, M. / Kurata, H. / Omi, R. / Kihara, Y. / Warshaviak, D. / Nakade, S. / Asmar-Rovira, G. / Mileni, M. ...Chrencik, J.E. / Roth, C.B. / Terakado, M. / Kurata, H. / Omi, R. / Kihara, Y. / Warshaviak, D. / Nakade, S. / Asmar-Rovira, G. / Mileni, M. / Mizuno, H. / Griffith, M.T. / Rodgers, C. / Han, G.W. / Velasquez, J. / Chun, J. / Stevens, R.C. / Hanson, M.A. / GPCR Network (GPCR)
CitationJournal: Cell / Year: 2015
Title: Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1.
Authors: Chrencik, J.E. / Roth, C.B. / Terakado, M. / Kurata, H. / Omi, R. / Kihara, Y. / Warshaviak, D. / Nakade, S. / Asmar-Rovira, G. / Mileni, M. / Mizuno, H. / Griffith, M.T. / Rodgers, C. / ...Authors: Chrencik, J.E. / Roth, C.B. / Terakado, M. / Kurata, H. / Omi, R. / Kihara, Y. / Warshaviak, D. / Nakade, S. / Asmar-Rovira, G. / Mileni, M. / Mizuno, H. / Griffith, M.T. / Rodgers, C. / Han, G.W. / Velasquez, J. / Chun, J. / Stevens, R.C. / Hanson, M.A.
History
DepositionMar 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysophosphatidic acid receptor 1,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4783
Polymers52,6141
Non-polymers8642
Water543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.610, 112.400, 155.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsauthors have indicated that the biological unit is unknown

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Components

#1: Protein Lysophosphatidic acid receptor 1,Soluble cytochrome b562 / LPA-1 / Lysophosphatidic acid receptor Edg-2 / Cytochrome b-562 / Cytochrome b-562 / LPA-1 / ...LPA-1 / Lysophosphatidic acid receptor Edg-2 / Cytochrome b-562 / Cytochrome b-562 / LPA-1 / Lysophosphatidic acid receptor Edg-2


Mass: 52614.219 Da / Num. of mol.: 1 / Mutation: M1007W, H1102I, R1106L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: LPAR1, EDG2, LPA1, cybC / Plasmid: pFASTBAC / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92633, UniProt: P0ABE7
#2: Chemical ChemComp-ON9 / 3-{1-[(2S,3S)-3-(4-acetyl-3,5-dimethoxyphenyl)-2-(2,3-dihydro-1H-inden-2-ylmethyl)-3-hydroxypropyl]-4-(methoxycarbonyl)-1H-pyrrol-3-yl}propanoic acid / ONO-9910539


Mass: 563.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H37NO8
#3: Chemical ChemComp-1WV / (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate


Mass: 300.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H32O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 0.1 M sodium citrate (pH 5.5), 34 - 38% (v/v) PEG400 and 200 mM ammonium acetate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.033
SYNCHROTRONAPS 23-ID-B21.033
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDDec 1, 2012
MARMOSAIC 300 mm CCD2CCDDec 20, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MirrorsSINGLE WAVELENGTHMx-ray1
2MirrorsSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21
ReflectionResolution: 2.9→47 Å / Num. obs: 11627 / % possible obs: 78 % / Redundancy: 2.6 % / Biso Wilson estimate: 61.28 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 4
Reflection shellResolution: 2.9→3.1 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1 / % possible all: 62

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ids 3V2Y and 4EIY

3v2y

4eiy


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.8895 / Cor.coef. Fo:Fc free: 0.8627 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.438
RfactorNum. reflection% reflectionSelection details
Rfree0.2791 584 5.02 %RANDOM
Rwork0.265 ---
obs0.2657 11627 81.9 %-
Displacement parametersBiso mean: 99.28 Å2
Baniso -1Baniso -2Baniso -3
1-4.3229 Å20 Å20 Å2
2---4.0348 Å20 Å2
3----0.2881 Å2
Refine analyzeLuzzati coordinate error obs: 0.708 Å
Refinement stepCycle: 1 / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 59 3 3039
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093103HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.924220HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1416SINUSOIDAL4
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes62HARMONIC2
X-RAY DIFFRACTIONt_gen_planes475HARMONIC5
X-RAY DIFFRACTIONt_it3103HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.63
X-RAY DIFFRACTIONt_other_torsion2.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion417SEMIHARMONIC5
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_contact3553SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.18 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2732 106 4.54 %
Rwork0.2685 2228 -
all0.2687 2334 -
obs--81.9 %
Refinement TLS params.Method: refined / Origin x: -0.3927 Å / Origin y: -18.87 Å / Origin z: 31.1438 Å
111213212223313233
T-0.304 Å2-0.0999 Å2-0.0203 Å2-0.304 Å20.0534 Å2--0.1997 Å2
L0.7326 °2-0.6175 °20.3548 °2-1.5606 °2-1.2685 °2--1.0154 °2
S-0.0489 Å °0.0053 Å °-0.1374 Å °-0.0997 Å °0.0812 Å °0.0111 Å °-0.0519 Å °-0.1653 Å °-0.0322 Å °
Refinement TLS groupSelection details: { A|* }

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