7TD2: Lysophosphatidic acid receptor 1-Gi complex

Lysophosphatidic acid receptor 1-Gi complex bound to LPA, state a. Determined by electron microscopy at 3.11 Å resolution. Released 9 Feb 2022.

Method: Electron microscopy
Resolution: 3.11 Å
Organisms: Homo sapiens, Bos taurus, Rattus norvegicus
Chains: 4
Atoms: 6,896
Mol. weight: 128.6 kDa
Ligands: NKP
Released: 9 Feb 2022

Explore 7TD2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TD2 contains 30 α-helices and 36 β-strands across 4 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	11-31	21
β-strand	33-39	7	8
α-helix	46-53	8
β-strand	185-191	7	8
β-strand	194-200	7	8
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-226	7	8
α-helix	228-230	3
β-strand	233	1	9
β-strand	241	1	9
α-helix	242-254	13
β-strand	263-269	7	8
α-helix	271-277	7
α-helix	283-285	3
α-helix	296-309	14
β-strand	319-323	5	8
α-helix	331-350	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	88-94	7	2
α-helix	95	1
β-strand	102-105	4	3
β-strand	111-115	5	3
β-strand	121-125	5	3
β-strand	134-139	6	3
β-strand	146-150	5	4
β-strand	156-161	6	4
β-strand	165-170	6	4
β-strand	176-181	6	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	207-212	6	5
β-strand	218-222	5	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	250-254	5	6
β-strand	260-264	5	6
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	304-308	5	7
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	335-339	5	1

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	27-29	3
α-helix	30-42	13
α-helix	53-55	3
α-helix	56-58	3

Chain R: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	30-36	7
α-helix	47-76	30
α-helix	83-105	23
α-helix	110-114	5
α-helix	118-150	33
α-helix	157-159	3
α-helix	161-180	20
α-helix	204-237	34
α-helix	252-283	32
α-helix	293-311	19
α-helix	316-321	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysophosphatidic acid receptor 1	R	protein	350	Homo sapiens	Q92633 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Bos taurus	P62871 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	379	Rattus norvegicus	P10824 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Bos taurus	P63212 (AlphaFold model)

Sequence of entity 1 (R), FASTA

>7TD2_1 Lysophosphatidic acid receptor 1 (chains R)
DYKDDDDKAAAAAISTSIPVISQPQFTAMNEPQCFYNESIAFFYNRSGKHLATEWNTVSK
LVMGLGITVCIFIMLANLLVMVAIYVNRRFHFPIYYLMANLAAADFFAGLAYFYLMFNTG
PNTRRLTVSTWLLRQGLIDTSLTASVANLLAIAIERHITVFRMQLHTRMSNRRVVVVIVV
IWTMAIVMGAIPSVGWNCICDIENCSNMAPLYSDSYLVFWAIFNLVTFVVMVVLYAHIFG
YVRQRTMRMSRHSSGPRRNRDTMMSLLKTVVIVLGAFIICWTPGLVLLLLDVCCPQCDVL
AYEKFFLLLAEFNSAMNPIIYSYRDKEMSATFRQILCCQRSENPTGPTEG

Sequence of entity 2 (B), FASTA

>7TD2_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (A), FASTA

>7TD2_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGSSHHHHHHSSGLEVLFQGPHMASMGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVK
LLLLGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDF
GDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYY
LNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCF
EGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFE
EKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFV
FDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (G), FASTA

>7TD2_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFSAIL

Ligands and cofactors

ID	Name	Formula	Copies
NKP	(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate	C21 H41 O7 P	1

Primary citation

Differential activation mechanisms of lipid GPCRs by lysophosphatidic acid and sphingosine 1-phosphate. Liu, S., Paknejad, N., Zhu, L. et al. Nat Commun (2022) 13:731-731. DOI 10.1038/s41467-022-28417-2 · 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
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…
7YU5 3.7 Å, Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, state1

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