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- EMDB-64542: Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1... -

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Basic information

Entry
Database: EMDB / ID: EMD-64542
TitleCryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425
Map data
Sample
  • Complex: Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425
    • Protein or peptide: Lysophosphatidic acid receptor 2,ARK1
  • Ligand: 3-[[4-[4-[[(1~{R})-1-(2-chlorophenyl)ethoxy]carbonylamino]-3-methyl-1,2-oxazol-5-yl]phenyl]methylsulfanyl]propanoic acid
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsGPCR / LPA2 / Lysophosphatidic acid receptor 2 / Ki16425 / ARK1 / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / Resolution: 2.99 Å
AuthorsKojima A / Kawakami K / Kobayashi K / Matsui TE / Uemoto K / Fukuda M / Kato HE
Funding support Japan, 6 items
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 TE / Uemoto K / Gu Y / Fukuda M / Kato HE
History
DepositionMay 11, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64542.png

Downloads & links

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Map

FileDownload / File: emd_64542.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 350 pix.
= 290.5 Å		0.83 Å/pix.
x 350 pix.
= 290.5 Å		0.83 Å/pix.
x 350 pix.
= 290.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.34410805 - 0.66848874
Average (Standard dev.)0.000102211685 (±0.013146839)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 290.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64542_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_64542_additional_1.map
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Half map: #2

Fileemd_64542_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_64542_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1...

EntireName: Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425
Components
  • Complex: Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425
    • Protein or peptide: Lysophosphatidic acid receptor 2,ARK1
  • Ligand: 3-[[4-[4-[[(1~{R})-1-(2-chlorophenyl)ethoxy]carbonylamino]-3-methyl-1,2-oxazol-5-yl]phenyl]methylsulfanyl]propanoic acid
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1...

SupramoleculeName: Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Lysophosphatidic acid receptor 2,ARK1

MacromoleculeName: Lysophosphatidic acid receptor 2,ARK1 / type: protein_or_peptide / ID: 1 / Details: Lysophosphatidic acid receptor 2 (LPA2)-ARK1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.158406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAENLYFQ GMGQCYYNET IGFFYNNSGK ELSSHWRPKD VVVVALGLTV SVLVLLTNLL VIAAIASNR RFHQPIYYLL GNLAAADLFA GVAYLFLMFH TGPRTARLSL EGWFLRQGLL DTSLTASVAT LLAIAVERHR S VMAVQLHS ...String:
MKTIIALSYI FCLVFADYKD DDDAENLYFQ GMGQCYYNET IGFFYNNSGK ELSSHWRPKD VVVVALGLTV SVLVLLTNLL VIAAIASNR RFHQPIYYLL GNLAAADLFA GVAYLFLMFH TGPRTARLSL EGWFLRQGLL DTSLTASVAT LLAIAVERHR S VMAVQLHS RLPRGRVVML IVGVWVAALG LGLLPAHSWH CLCALDRCSR MAPLLSRSYL AVWALSSLLV FLLMVAVYTR IF FYVRRRV QRMLELRRLL REQGEKLLKL AEESEKKIKE AIEKGEDVVK VATEETHKLI KAIWESSFEV ARLLGVPEEV LEK FRKELE KLLEESKKRI EEAIKKGEDV LKVVEEEAKK LREHSEKFLE TARSLGVDPR PLERLARIVR VVEESLVRIV KAIK EGEDV EKVLLSESTL IKSSIILSSG LDPREAYEEL LATYEETRDS ELVKEFVELV RELLRLRGEP EELVRQLDKL IEAID RMEK AVAEGEDTLP LFLELAREIL KALSDVARIL AEREGLDVEL IDEIVDTASR LLEEVIKKAK EGEDLDEEEE KVKKEL EEL KKRTEERARA LGQDVELVRT IVDSLSTLLS EIVEGIKRVK EGEDPLEVLA RVVLTATLQI LELVRTAERR RRERTLS LV KTVVIILGAF VVCWTPGQVV LLLDGLGCES CNVLAVEKYF LLLAEANSLV NAAVYSCRDA EMRRTFRRLL CCACLRQS T RESVHYTSSA QGGASTRIML PENGHPLMDS TLLEVLFQ

UniProtKB: Lysophosphatidic acid receptor 2, Lysophosphatidic acid receptor 2

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Macromolecule #2: 3-[[4-[4-[[(1~{R})-1-(2-chlorophenyl)ethoxy]carbonylamino]-3-meth...

MacromoleculeName: 3-[[4-[4-[[(1~{R})-1-(2-chlorophenyl)ethoxy]carbonylamino]-3-methyl-1,2-oxazol-5-yl]phenyl]methylsulfanyl]propanoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1L9P
Molecular weightTheoretical: 474.957 Da

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 151855
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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