7YU4: Lysophosphatidic acid receptor 1

Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, focused on receptor. Determined by electron microscopy at 3.7 Å resolution. Released 5 Oct 2022.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,050
Mol. weight: 43.35 kDa
Ligands: K6L
Released: 5 Oct 2022

Explore 7YU4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YU4 contains 10 α-helices and 0 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	30-36	7
α-helix	47-76	30
α-helix	84-105	22
α-helix	110-115	6
α-helix	118-149	32
α-helix	162-184	23
α-helix	204-229	26
α-helix	257-283	27
α-helix	293-310	18
α-helix	316-321	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysophosphatidic acid receptor 1	A	protein	379	Homo sapiens	Q92633 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7YU4_1 Lysophosphatidic acid receptor 1 (chains A)
DYKDDDDAMGAAISTSIPVISQPQFTAMNEPQCFYNESIAFFYNRSGKHLATEWNTVSKL
VMGLGITVCIFIMLANLLVMVAIYVNRRFHFPIYYLMANLAAADFFAGLAYFYLMFNTGP
NTRRLTVSTWLLRQGLIDTSLTASVANLLAIAIERHITVFRMQLHTRMSNRRVVVVIVVI
WTMAIVMGAIPSVGWNCICDIENCSNMAPLYSDSYLVFWAIFNLVTFVVMVVLYAHIFGY
VRQRTMRMSRHSSGPRRNRDTMMSLLKTVVIVLGAFIICWTPGLVLLLLDVCCPQCDVLA
YEKFFLLLAEFNSAMNPIIYSYRDKEMSATFRQILCCQRSENPTGPTEGSDRSASSLNHT
ILAGVHSNDHSVVENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
K6L	[(2~{R})-2-[5-(2-hexylphenyl)pentanoylamino]-3-oxidanyl-propyl] dihydrogen…	C20 H34 N O6 P	1

Primary citation

Structure of the active G i -coupled human lysophosphatidic acid receptor 1 complexed with a potent agonist. Akasaka, H., Tanaka, T., Sano, F.K. et al. Nat Commun (2022) 13:5417-5417. DOI 10.1038/s41467-022-33121-2 · PubMed

Other PDB entries of the same protein (UniProt Q92633 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7TD0 2.83 Å, Lysophosphatidic acid receptor 1-Gi complex bound to LPA
9J5V 2.86 Å, Human Lysophosphatidic Acid Receptor 1-Gi complex bound to CpY
4Z35 2.9 Å, Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO-9910539
4Z36 2.9 Å, Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO-3080573
4Z34 3.0 Å, Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO9780307
9IZG 3.04 Å, Cryo-EM structure of LPA1-Gq complex with LPA
9IZH 3.04 Å, Cryo-EM structure of LPA1-G13 complex with LPA
7TD1 3.08 Å, Lysophosphatidic acid receptor 1-Gi complex bound to LPA, state a
7TD2 3.11 Å, Lysophosphatidic acid receptor 1-Gi complex bound to LPA, state a
9IZF 3.14 Å, Cryo-EM structure of LPA1-Gi complex with LPA
7YU3 3.5 Å, Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556
7YU5 3.7 Å, Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, state1

Browse structure collections

About this viewer

MolViewer shows 7YU4 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.