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- PDB-4z36: Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in co... -

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Basic information

Entry
Database: PDB / ID: 4z36
TitleCrystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO-3080573
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) / novel disulfide bond engineering / 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 / calmodulin dependent kinase signaling pathway / 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 / calmodulin dependent kinase signaling pathway / Lysosphingolipid and LPA receptors / lysophosphatidic acid binding / negative regulation of cilium assembly / regulation of synaptic vesicle cycle / corpus callosum development / bleb assembly / oligodendrocyte development / cellular response to oxygen levels / regulation of metabolic process / optic nerve development / negative regulation of cAMP-mediated signaling / regulation of postsynaptic neurotransmitter receptor internalization / 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 / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / myelination / cell chemotaxis / neurogenesis / cerebellum development / dendritic shaft / electron transport chain / G protein-coupled receptor activity / PDZ domain binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of neuron projection development / presynaptic membrane / regulation of cell shape / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / 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-ON3 / Soluble cytochrome b562 / Lysophosphatidic acid receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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

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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)52,6613
Polymers51,8421
Non-polymers8192
Water543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.350, 111.930, 153.960
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: 51842.332 Da / Num. of mol.: 1
Fragment: unp residues 2-232; unp residues 23-64; unp residues 78-127; unp residues 249-327
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-ON3 / 1-(4-{[(2S,3R)-2-(2,3-dihydro-1H-inden-2-yloxy)-3-(3,5-dimethoxy-4-methylphenyl)-3-hydroxypropyl]oxy}phenyl)cyclopropanecarboxylic acid / ONO-3080573


Mass: 518.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H34O7
#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 / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.47 %
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 CCD1CCDNov 10, 2013
MARMOSAIC 300 mm CCD2CCDNov 30, 2013
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: 12701 / % possible obs: 92 % / Redundancy: 5.4 % / Biso Wilson estimate: 66.4 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.2
Reflection shellResolution: 2.9→3.1 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.3 / % possible all: 80

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.8849 / Cor.coef. Fo:Fc free: 0.848 / SU R Cruickshank DPI: 2.352 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 4.569 / SU Rfree Blow DPI: 0.426 / SU Rfree Cruickshank DPI: 0.429
RfactorNum. reflection% reflectionSelection details
Rfree0.2921 625 4.94 %RANDOM
Rwork0.2718 ---
obs0.2728 12660 91.11 %-
Displacement parametersBiso mean: 95.32 Å2
Baniso -1Baniso -2Baniso -3
1-11.8945 Å20 Å20 Å2
2---7.1017 Å20 Å2
3----4.7928 Å2
Refine analyzeLuzzati coordinate error obs: 0.684 Å
Refinement stepCycle: 1 / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 56 3 3074
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093141HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.874267HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1445SINUSOIDAL4
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes62HARMONIC2
X-RAY DIFFRACTIONt_gen_planes476HARMONIC5
X-RAY DIFFRACTIONt_it3141HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.58
X-RAY DIFFRACTIONt_other_torsion2.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion419SEMIHARMONIC5
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_contact3662SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.18 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2793 117 4.51 %
Rwork0.2562 2476 -
all0.2572 2593 -
obs--91.11 %
Refinement TLS params.Method: refined / Origin x: -0.3047 Å / Origin y: -18.8188 Å / Origin z: 30.2925 Å
111213212223313233
T-0.1899 Å2-0.1437 Å2-0.0055 Å2-0.198 Å20.0353 Å2--0.1326 Å2
L0.7166 °2-0.6523 °20.216 °2-0.8696 °2-0.7267 °2--0.3715 °2
S-0.0088 Å °-0.0203 Å °-0.1395 Å °-0.102 Å °0.1233 Å °-0.0956 Å °-0.0382 Å °-0.0319 Å °-0.1145 Å °
Refinement TLS groupSelection details: { A|* }

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