9VO1: Gi coupled Sphingosine 1-phosphate receptor

Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with SAR247799. Determined by electron microscopy at 2.97 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 2.97 Å
Organisms: Homo sapiens, Mus musculus, Escherichia coli
Chains: 5
Atoms: 8,861
Mol. weight: 174.76 kDa
Ligands: A1LYQ
Released: 28 Jan 2026

Explore 9VO1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9VO1 contains 33 α-helices and 62 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: 4 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	12-23	12
α-helix	37-39	3
β-strand	46-50	5	1
β-strand	57-61	5	2
β-strand	68-73	6	2
β-strand	77-82	6	2
β-strand	87-93	7	2
α-helix	94	1
β-strand	99-104	6	3
β-strand	110-115	6	3
β-strand	120-124	5	3
β-strand	133-138	6	3
β-strand	145	1	4
β-strand	149-152	4	5
β-strand	155-157	3	5
β-strand	160	1	4
β-strand	164-169	6	5
β-strand	175-180	6	5
β-strand	186	1	6
β-strand	190-191	2	6
β-strand	197-202	6	6
β-strand	206-211	6	6
β-strand	219-221	3	6
β-strand	228	1	7
β-strand	232-233	2	8
β-strand	239-241	3	8
β-strand	244	1	7
β-strand	249-253	5	8
β-strand	259-263	5	8
β-strand	272-277	6	9
β-strand	283-288	6	9
β-strand	293-297	5	9
β-strand	303-306	4	9
β-strand	314-319	6	1
β-strand	326-330	5	1
β-strand	335-338	4	1

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-18	10
α-helix	30-41	12
α-helix	45-47	3
α-helix	54-55	2

Chain D: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
α-helix	33	1
β-strand	34-38	5	15
α-helix	40-41	2
α-helix	46-55	10
β-strand	185-191	7	15
β-strand	194-200	7	15
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	15
β-strand	233	1	16
β-strand	241	1	16
α-helix	242-254	13
β-strand	263-269	7	15
α-helix	271-278	8
α-helix	283-285	3
α-helix	297-303	7
α-helix	308-310	3
β-strand	319-323	5	15
α-helix	331-350	20

Chain E: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	17-24	8	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	68-73	6	10
β-strand	78-84	7	10
β-strand	92-99	8	11
β-strand	111	1	11
β-strand	115-117	3	11
β-strand	146-148	3	12
β-strand	155-159	5	13
β-strand	166	1	14
β-strand	172	1	14
β-strand	174-179	6	12
β-strand	186-190	5	12
β-strand	194-195	2	12
α-helix	196	1
β-strand	203-206	4	13
β-strand	212-216	5	13
β-strand	226-231	6	12
β-strand	243-246	4	12

Chain F: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	25-32	8
α-helix	49-72	24
α-helix	79-104	26
α-helix	107-111	5
α-helix	117-146	30
α-helix	157-175	19
α-helix	177-180	4
α-helix	200-228	29
α-helix	251-278	28
α-helix	290-292	3
α-helix	296-313	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	A	protein	357	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
scFv16	E	protein	251	Mus musculus
Soluble cytochrome b562,Sphingosine 1-phosphate receptor 1	F	protein	534	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), P21453 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	D	protein	354	Homo sapiens	P63096

Sequence of entity 1 (A), FASTA

>9VO1_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains A)
HHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRI
QMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTC
AYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGD
TTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFT
GHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGR
LLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (C), FASTA

>9VO1_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (E), FASTA

>9VO1_3 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAA

Sequence of entity 4 (F), FASTA

>9VO1_4 Soluble cytochrome b562,Sphingosine 1-phosphate receptor 1 (chains F)
MKTIIALSYIFCLVFADYKDDDDKLEVLFQGPGSADLEDNWETLNDNLKVIEKADNAAQV
KDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKE
AQAAAEQLKTTRNAYIQKYLMGPTSVPLVKAHRSSVSDYVNYDIIVRHYNYTGKLNISAD
KENSIKLTSVVFILICCFIILENIFVLLTIWKTKKFHRPMYYFIGNLALSDLLAGVAYTA
NLLLSGATTYKLTPAQWFLREGSMFVALSASVFSLLAIAIERYITMLKMKLHNGSNNFRL
FLLISACWVISLILGGLPIMGWNCISALSSCSTVLPLYHKHYILFCTTVFTLLLLSIVIL
YCRIYSLVRTRSRRLTFRKNISKASRSSEKSLALLKTVIIVLSVFIACWAPLFILLLLDV
GCKVKTCDILFRAEYFLVLAVLNSGTNPIIYTLTNKEMRRAFIRIMSCCKCPSGDSAGKF
KRPIIAGMEFSRSKSDNSSHPQKDEGDNPETIMSSGNVNSSSLEHHHHHHHHHH

Sequence of entity 5 (D), FASTA

>9VO1_5 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains D)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Ligands and cofactors

ID	Name	Formula	Copies
A1LYQ	SAR247799	C21 H16 Cl N3 O5	1

Primary citation

Structural insights into subtype-specific agonist recognition by sphingosine-1-phosphate receptors. Yu, L., Jiao, H., Pang, B. et al. PLoS Biol (2026) 24:e3003381-e3003381. DOI 10.1371/journal.pbio.3003381 · 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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