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- PDB-9uvz: Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1... -

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Basic information

Entry
Database: PDB / ID: 9uvz
TitleCryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425
ComponentsLysophosphatidic acid receptor 2,ARK1
KeywordsMEMBRANE PROTEIN / GPCR / LPA2 / Lysophosphatidic acid receptor 2 / Ki16425 / ARK1
Function / homology
Function and homology information


lysophosphatidic acid receptor activity / Lysosphingolipid and LPA receptors / positive regulation of Rho protein signal transduction / presynaptic active zone membrane / PDZ domain binding / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (q) signalling events ...lysophosphatidic acid receptor activity / Lysosphingolipid and LPA receptors / positive regulation of Rho protein signal transduction / presynaptic active zone membrane / PDZ domain binding / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (q) signalling events / positive regulation of MAPK cascade / G protein-coupled receptor signaling pathway / lipid binding / glutamatergic synapse / cell surface / plasma membrane / cytoplasm
Similarity search - Function
Lysophosphatidic acid receptor EDG-4 / Lysophosphatidic acid receptor / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
: / Lysophosphatidic acid receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 2.99 Å
AuthorsKojima, A. / Kawakami, K. / Kobayashi, K. / Matsui, T.E. / Uemoto, K. / Fukuda, M. / Kato, H.E.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJAX222F Japan
Japan Science and TechnologyJPMJPR24OF Japan
Japan Society for the Promotion of Science (JSPS)25K09525 Japan
Japan Society for the Promotion of Science (JSPS)24H02262 Japan
Japan Society for the Promotion of Science (JSPS)25H01338 Japan
Japan Society for the Promotion of Science (JSPS)JP24KJ0981 Japan
CitationJournal: Biorxiv / Year: 2026
Title: A Rapid and Universal Pipeline for High-Resolution GPCR Structure Determination through In Silico Construct Optimization and de novo Protein Design
Authors: Kojima, A. / Kawakami, K. / Kobayashi, N. / Kobayashi, K. / Matsui, T.E. / Uemoto, K. / Gu, Y. / Fukuda, M. / Kato, H.E.
History
DepositionMay 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysophosphatidic acid receptor 2,ARK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6563
Polymers86,1581
Non-polymers4982
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Lysophosphatidic acid receptor 2,ARK1 / LPA receptor 2 / LPA-2 / Lysophosphatidic acid receptor Edg-4


Mass: 86158.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Lysophosphatidic acid receptor 2 (LPA2)-ARK1
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: LPAR2, EDG4, LPA2 / Production host: Homo sapiens (human) / References: UniProt: Q9HBW0
#2: Chemical ChemComp-A1L9P / 3-[[4-[4-[[(1~{R})-1-(2-chlorophenyl)ethoxy]carbonylamino]-3-methyl-1,2-oxazol-5-yl]phenyl]methylsulfanyl]propanoic acid / (R)-KI16425


Mass: 474.957 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23ClN2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21syntheic construct32630
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 45.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: REFMAC / Version: 5.8.0425 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151855 / Symmetry type: POINT
RefinementResolution: 2.99→2.99 Å / Cor.coef. Fo:Fc: 0.817 / WRfactor Rwork: 0.399 / SU B: 10.439 / SU ML: 0.178 / Average fsc free: 0 / Average fsc overall: 0.6518 / Average fsc work: 0.6518 / ESU R: 0.324
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3988 82728 -
all0.399 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 78.07 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0125555
ELECTRON MICROSCOPYr_bond_other_d00.0165652
ELECTRON MICROSCOPYr_angle_refined_deg1.7561.8827498
ELECTRON MICROSCOPYr_angle_other_deg0.6661.76412974
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.3165683
ELECTRON MICROSCOPYr_dihedral_angle_2_deg8.4892.92365
ELECTRON MICROSCOPYr_dihedral_angle_other_2_deg40.62712.52
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.079101089
ELECTRON MICROSCOPYr_dihedral_angle_6_deg11.41910239
ELECTRON MICROSCOPYr_chiral_restr0.090.2898
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.026454
ELECTRON MICROSCOPYr_gen_planes_other0.0030.021220
ELECTRON MICROSCOPYr_nbd_refined0.2260.21328
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1510.25090
ELECTRON MICROSCOPYr_nbtor_refined0.1710.22794
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0660.23316
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1280.294
ELECTRON MICROSCOPYr_mcbond_it7.3836.572732
ELECTRON MICROSCOPYr_mcbond_other7.3836.5692732
ELECTRON MICROSCOPYr_mcangle_it11.35311.8523415
ELECTRON MICROSCOPYr_mcangle_other11.35211.8573416
ELECTRON MICROSCOPYr_scbond_it12.4078.7872823
ELECTRON MICROSCOPYr_scbond_other12.4058.7872822
ELECTRON MICROSCOPYr_scangle_it20.78215.1624083
ELECTRON MICROSCOPYr_scangle_other20.77915.1624084
ELECTRON MICROSCOPYr_lrange_it26.1783.45323557
ELECTRON MICROSCOPYr_lrange_other26.17383.45323557
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.7-2.771.19661421.19661420.1221.196
2.77-2.8460.85659760.85659760.1620.856
2.846-2.9280.89758470.89758470.270.897
2.928-3.0190.955840.955840.360.9
3.019-3.1170.80154540.80154540.4650.801
3.117-3.2270.60652880.60652880.5810.606
3.227-3.3490.48350640.48350640.6840.483
3.349-3.4850.38949490.38949490.7780.389
3.485-3.640.32846880.32846880.8710.328
3.64-3.8180.34345230.34345230.9270.343
3.818-4.0240.35242160.35242160.9510.352
4.024-4.2680.33340630.33340630.9660.333
4.268-4.5620.30937560.30937560.970.309
4.562-4.9270.27935610.27935610.9660.279
4.927-5.3970.24232440.24232440.9530.242
5.397-6.0330.26429460.26429460.9140.264
6.033-6.9640.37225930.37225930.8560.372
6.964-8.5230.37122160.37122160.8690.371
8.523-12.030.26616850.26616850.9440.266
12.03-136.120.8499330.8499330.9460.849

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