7YU8: Lysophosphatidic acid receptor 1

Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, state4. Determined by electron microscopy at 5.6 Å resolution. Released 5 Oct 2022.

Method: Electron microscopy
Resolution: 5.6 Å
Organisms: Homo sapiens, Rattus norvegicus, Bos taurus
Chains: 5
Atoms: 8,755
Mol. weight: 157.78 kDa
Ligands: K6L
Released: 5 Oct 2022

Explore 7YU8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YU8 contains 35 α-helices and 58 β-strands across 5 chains. 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: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-40	7	1
α-helix	42-44	3
α-helix	46-53	8
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-229	3
α-helix	242-254	13
α-helix	257-259	3
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	296-307	12
β-strand	319-323	5	1
α-helix	331-350	20

Chain B: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
α-helix	95	1
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	175-180	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	218-223	6	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	260-264	5	7
α-helix	272	1
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	318-320	3	2
β-strand	327-329	3	2
β-strand	336-339	4	2

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain R: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	30-36	7
α-helix	47-76	30
α-helix	83-105	23
α-helix	110-115	6
α-helix	118-151	34
α-helix	162-184	23
α-helix	204-237	34
α-helix	253-283	31
α-helix	293-310	18
α-helix	316-320	5

Chain S: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-12	3	10
β-strand	19-24	6	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	68-73	6	9
α-helix	74-76	3
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	110-111	2	10
β-strand	115-119	5	10
β-strand	140-141	2	11
β-strand	147-148	2	12
β-strand	155-161	7	11
β-strand	166	1	13
β-strand	172	1	13
β-strand	174-179	6	14
β-strand	186-189	4	14
β-strand	203-208	6	11
β-strand	211-216	6	11
β-strand	226-231	6	14
β-strand	239	1	14
β-strand	243-244	2	14
β-strand	245-246	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysophosphatidic acid receptor 1	R	protein	379	Homo sapiens	Q92633 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	351	Rattus norvegicus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	68	Bos taurus	P63212 (AlphaFold model)
scFv16	S	protein	260	Mus musculus

Sequence of entity 1 (R), FASTA

>7YU8_1 Lysophosphatidic acid receptor 1 (chains R)
DYKDDDDAMGAAISTSIPVISQPQFTAMNEPQCFYNESIAFFYNRSGKHLATEWNTVSKL
VMGLGITVCIFIMLANLLVMVAIYVNRRFHFPIYYLMANLAAADFFAGLAYFYLMFNTGP
NTRRLTVSTWLLRQGLIDTSLTASVANLLAIAIERHITVFRMQLHTRMSNRRVVVVIVVI
WTMAIVMGAIPSVGWNCICDIENCSNMAPLYSDSYLVFWAIFNLVTFVVMVVLYAHIFGY
VRQRTMRMSRHSSGPRRNRDTMMSLLKTVVIVLGAFIICWTPGLVLLLLDVCCPQCDVLA
YEKFFLLLAEFNSAMNPIIYSYRDKEMSATFRQILCCQRSENPTGPTEGSDRSASSLNHT
ILAGVHSNDHSVVENLYFQ

Sequence of entity 2 (A), FASTA

>7YU8_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>7YU8_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G), FASTA

>7YU8_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFS

Sequence of entity 5 (S), FASTA

>7YU8_5 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAASSEDLYFQ

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
7YU4 3.7 Å, Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, focused on…

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