9IZG: LPA1-Gq complex with LPA

Cryo-EM structure of LPA1-Gq complex with LPA. Determined by electron microscopy at 3.04 Å resolution. Released 1 Jan 2025.

Method: Electron microscopy
Resolution: 3.04 Å
Organisms: Homo sapiens, Mus musculus, Escherichia coli
Chains: 5
Atoms: 8,702
Mol. weight: 177.68 kDa
Ligands: NKP
Released: 1 Jan 2025

Explore 9IZG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IZG contains 33 α-helices and 65 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	7-25	19
β-strand	33-40	8	10
α-helix	42-44	3
α-helix	46-48	3
β-strand	70-76	7	10
β-strand	79-85	7	10
β-strand	105-111	7	10
α-helix	118-129	12
β-strand	138-144	7	10
α-helix	146-154	9
α-helix	160-163	4
α-helix	165-169	5
α-helix	170-174	5
α-helix	177-179	3
α-helix	184-203	20
β-strand	211-215	5	10
α-helix	223-242	20

Chain B: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
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
β-strand	100-105	6	3
β-strand	111-116	6	3
β-strand	120-125	6	3
β-strand	134-140	7	3
β-strand	146-151	6	4
β-strand	156-161	6	4
β-strand	165-170	6	4
β-strand	175-181	7	4
β-strand	187	1	5
β-strand	191-192	2	6
β-strand	198-202	5	6
β-strand	203	1	5
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-264	6	7
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	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	30-43	14
α-helix	56-58	3

Chain R: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	30-36	7
α-helix	47-76	30
α-helix	78-80	3
α-helix	83-106	24
α-helix	118-151	34
α-helix	162-180	19
β-strand	195	1	9
β-strand	203	1	9
α-helix	204-236	33
α-helix	247-269	23
α-helix	272-279	8
α-helix	293-310	18
α-helix	316-323	8

Chain S: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	17-25	9	11
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-51	7	13
α-helix	53-55	3
β-strand	58-60	3	13
β-strand	65	1	11
β-strand	68-73	6	11
β-strand	78-84	7	11
α-helix	88-90	3
β-strand	93-99	7	13
β-strand	111	1	13
β-strand	115-116	2	13
β-strand	117-119	3	12
β-strand	128-129	2	14
β-strand	134-136	3	15
β-strand	143-147	5	16
β-strand	148-149	2	14
β-strand	154	1	17
β-strand	160	1	17
β-strand	162-167	6	15
β-strand	174-178	5	15
β-strand	182-183	2	15
α-helix	184	1
β-strand	191-196	6	16
β-strand	199-204	6	16
β-strand	214-219	6	15
α-helix	225	1
β-strand	227	1	15
β-strand	231-234	4	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	382	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	70	Mus musculus	P63213 (AlphaFold model)
Soluble cytochrome b562,Lysophosphatidic acid receptor 1,LgBiT tag	R	protein	651	Escherichia coli, Homo sapiens, synthetic construct	P0ABE7 (AlphaFold model), Q92633 (AlphaFold model)
Gs-mini-Gq chimera	A	protein	246	Homo sapiens	A0A590UJY2
scFv16	S	protein	248	synthetic construct

Sequence of entity 1 (B), FASTA

>9IZG_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHHHENLYFQGSSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQ
MRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCA
YAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDT
TCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTG
HESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRL
LLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGGSG
GGGSGGSSSGGVSGWRLFKKIS

Sequence of entity 2 (C), FASTA

>9IZG_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Sequence of entity 3 (R), FASTA

>9IZG_3 Soluble cytochrome b562,Lysophosphatidic acid receptor 1,LgBiT tag (chains R)
MKTIIALSYIFCLVFADYKDDDDKADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAA
ALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKT
TRNAYIQKYLAAISTSIPVISQPQFTAMNEPQCFYNESIAFFYNRSGKHLATEWNTVSKL
VMGLGITVCIFIMLANLLVMVAIYVNRRFHFPIYYLMANLAAADFFAGLAYFYLMFNTGP
NTRRLTVSTWLLRQGLIDTSLTASVANLLAIAIERHITVFRMQLHTRMSNRRVVVVIVVI
WTMAIVMGAIPSVGWNCICDIENCSNMAPLYSDSYLVFWAIFNLVTFVVMVVLYAHIFGY
VRQRTMRMSRHSSGPRRNRDTMMSLLKTVVIVLGAFIICWTPGLVLLLLDVCCPQCDVLA
YEKFFLLLAEFNSAMNPIIYSYRDKEMSATFRQILCCQRSENPTGPTEGSDRSASSLNHT
ILAGVHSNDHSVVVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVR
SGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNM
LNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINS

Sequence of entity 4 (A), FASTA

>9IZG_4 Gs-mini-Gq chimera (chains A)
MGSTVSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGS
GGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNL
REYNLV

Sequence of entity 5 (S), FASTA

>9IZG_5 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

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

Structural insights into the engagement of lysophosphatidic acid receptor 1 with different G proteins. Suzuki, S., Tanaka, K., Kamegawa, A. et al. J Struct Biol (2024) 217:108164-108164. DOI 10.1016/j.jsb.2024.108164 · PubMed

Other PDB entries of the same protein (UniProt P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex

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