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- PDB-4z34: Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in co... -

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Basic information

Entry
Database: PDB / ID: 4z34
TitleCrystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO9780307
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 / oligodendrocyte development ...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 / oligodendrocyte development / bleb assembly / negative regulation of cAMP-mediated signaling / 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 / neurogenesis / cerebellum development / cell chemotaxis / dendritic shaft / G protein-coupled receptor activity / PDZ domain binding / 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 / positive regulation of canonical NF-kappaB signal transduction / postsynaptic membrane / positive regulation of MAPK cascade / dendritic spine / periplasmic space / electron transfer activity / endosome / positive regulation of apoptotic process / iron ion binding / 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-ON7 / 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: 3 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 / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,4363
Polymers52,6141
Non-polymers8222
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.280, 112.150, 154.630
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
Fragment: unp residues 2-232; unp residues 23-64; unp residues 73-127; unp residues 248-326
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-ON7 / {1-[(2S,3S)-2-(2,3-dihydro-1H-inden-2-ylmethyl)-3-(3,5-dimethoxy-4-methylphenyl)-3-hydroxypropyl]-4-(methoxycarbonyl)-1 H-pyrrol-3-yl}acetic acid / ONO9780307


Mass: 521.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H35NO7
#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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.55 %
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 CCD1CCDJun 5, 2012
MARMOSAIC 300 mm CCD2CCDJun 19, 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: 3→45 Å / Num. obs: 10576 / % possible obs: 85 % / Redundancy: 4 % / Biso Wilson estimate: 37.83 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.7
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.4 / % possible all: 75

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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: 3→30 Å / Cor.coef. Fo:Fc: 0.8253 / Cor.coef. Fo:Fc free: 0.7754 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.475
RfactorNum. reflection% reflectionSelection details
Rfree0.2805 531 5.02 %RANDOM
Rwork0.2543 ---
obs0.2556 10576 83.6 %-
Displacement parametersBiso mean: 78.03 Å2
Baniso -1Baniso -2Baniso -3
1--3.0953 Å20 Å20 Å2
2---1.5013 Å20 Å2
3---4.5966 Å2
Refine analyzeLuzzati coordinate error obs: 0.579 Å
Refinement stepCycle: 1 / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 56 0 3047
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013113HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084234HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1424SINUSOIDAL4
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes63HARMONIC2
X-RAY DIFFRACTIONt_gen_planes475HARMONIC5
X-RAY DIFFRACTIONt_it3113HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.08
X-RAY DIFFRACTIONt_other_torsion2.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion422SEMIHARMONIC5
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_contact3594SEMIHARMONIC4
LS refinement shellResolution: 3→3.35 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.267 131 5.06 %
Rwork0.2404 2460 -
all0.2418 2591 -
obs--83.6 %
Refinement TLS params.Method: refined / Origin x: -0.4492 Å / Origin y: -18.8645 Å / Origin z: 31.0201 Å
111213212223313233
T-0.304 Å2-0.1247 Å2-0.0276 Å2-0.2548 Å2-0.016 Å2--0.2089 Å2
L0.6849 °2-0.3199 °20.1559 °2-0.7507 °2-0.8961 °2--0.9927 °2
S-0.0245 Å °0.0825 Å °-0.3207 Å °-0.0163 Å °0.2294 Å °0.0434 Å °-0.0464 Å °-0.1408 Å °-0.2049 Å °
Refinement TLS groupSelection details: { A|* }

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