9VJ6: 5-HT1AR-Gi3

Cryo-EM structure of 5-HT1AR-Gi3 in complex with F-15599. Determined by electron microscopy at 2.62 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 2.62 Å
Organisms: Homo sapiens, Mus musculus, Escherichia coli
Chains: 5
Atoms: 8,818
Mol. weight: 177.59 kDa
Ligands: CLR, T7M, A1ESC
Released: 12 Nov 2025

Explore 9VJ6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9VJ6 contains 39 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 B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-39	7	1
α-helix	46-53	8
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	331-350	20

Chain C: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	89-94	6	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	175-180	6	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	218-222	5	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
α-helix	272	1
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	303-308	6	9
β-strand	317-320	4	3
β-strand	327-330	4	3
β-strand	336-339	4	3

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	27-29	3
α-helix	30-44	15
α-helix	45-47	3
α-helix	53-55	3

Chain E: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
α-helix	53-55	3
β-strand	58-60	3	11
β-strand	65	1	10
β-strand	68-73	6	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	110-111	2	11
β-strand	115-119	5	11
β-strand	128-129	2	12
β-strand	135-136	2	13
β-strand	143-149	7	12
β-strand	154	1	14
β-strand	160	1	14
β-strand	162-167	6	15
β-strand	173-177	5	15
β-strand	183	1	15
α-helix	184	1
β-strand	191-196	6	12
β-strand	199-204	6	12
α-helix	209-211	3
β-strand	214-219	6	15
β-strand	227	1	15
β-strand	231-232	2	15
β-strand	233-234	2	13

Chain R: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	35-63	29
α-helix	65-67	3
α-helix	70-88	19
α-helix	90-99	10
α-helix	106-139	34
α-helix	141-146	6
α-helix	150-168	19
α-helix	170-173	4
α-helix	193-200	8
α-helix	201-205	5
α-helix	206-227	22
α-helix	324-367	44
α-helix	368-370	3
α-helix	379-397	19
α-helix	398-402	5
α-helix	405-412	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-3	B	protein	354	Homo sapiens	P08754 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	358	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Homo sapiens	P59768 (AlphaFold model)
ScFv16	E	protein	251	Mus musculus
Soluble cytochrome b562,5-hydroxytryptamine receptor 1A	R	protein	549	Escherichia coli, Homo sapiens	P08908 (AlphaFold model), P0ABE7

Sequence of entity 1 (B), FASTA

>9VJ6_1 Guanine nucleotide-binding protein G(i) subunit alpha-3 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAKEVKLLLLGAGESGKNTIVKQMKIIHEDG
YSEDECKQYKVVVYSNTIQSIIAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMT
PELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDRISQSNYIPTQQDVLRTRVK
TTGIVETHFTFKDLYFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRSPLTICYPEYTGSNTYEEAA
AYIQCQFEDLNRRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKECGLY

Sequence of entity 2 (C), FASTA

>9VJ6_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (D), FASTA

>9VJ6_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (E), FASTA

>9VJ6_4 ScFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAA

Sequence of entity 5 (R), FASTA

>9VJ6_5 Soluble cytochrome b562,5-hydroxytryptamine receptor 1A (chains R)
DYKDDDDAKLQTMHHHHHHHHHHENLYFQGGTTMADLEDNWETLNDNLKVIEKADNAAQV
KDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKE
AQAAAEQLKTTRNAYIQKYLGSTLEVLFQGPTTGISDVTVSYQVITSLLLGTLIFCAVLG
NACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFI
ALDVLCCTSSIWHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPML
GWRTPEDRSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKV
EKTGADTRHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVI
EVHRVGNSKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGT
FILCWLPFFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKK
IIKCKFCRQ

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2
T7M	(2R)-1-(heptadecanoyloxy)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahyd…	C46 H82 O16 P2	1
A1ESC	(3-chloranyl-4-fluoranyl-phenyl)-[4-fluoranyl-4-[[(5-methylpyrimidin-2-yl)methy…	C19 H21 Cl F2 N4 O	1

Primary citation

Pathway-selective 5-HT 1A R agonist as a rapid antidepressant strategy. Wang, C., Zhang, N., Shao, Y. et al. Cell (2025) 188:7222-7237.e24. DOI 10.1016/j.cell.2025.10.022 · PubMed

Other PDB entries of the same protein (UniProt P08754 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ODE 1.9 Å, Crystal structure of the heterodimeric complex of human RGS8 and activated Gi alpha 3
9YCX 2.1 Å, Neurotensin Receptor 1 (NTSR1) bound to Octotensin in complex with Gi3 in the…
9YCY 2.2 Å, Neurotensin Receptor 1 (NTSR1) bound to Octotensin in complex with Gi3 in the Canonical…
8IKL 2.33 Å, Cryo-EM structure of the CD97-G13 complex
8YK0 2.4 Å, Cryo-EM structure of human GPR156-Gi3 complex
7T10 2.5 Å, CryoEM structure of somatostatin receptor 2 in complex with somatostatin-14 and Gi3
7T11 2.7 Å, CryoEM structure of somatostatin receptor 2 in complex with Octreotide and Gi3.
9VJF 2.7 Å, Cryo-EM structure of 5-HT1AR-Gi3 in complex with buspirone
2IHB 2.71 Å, Crystal structure of the heterodimeric complex of human RGS10 and activated Gi alpha 3
2V4Z 2.8 Å, The crystal structure of the human G-protein subunit alpha (GNAI3) in complex with an…
7KH0 2.8 Å, Cryo-EM structure of the human arginine vasopressin AVP-vasopressin receptor V2R-Gs…
4G5O 2.9 Å, Structure of LGN GL4/Galphai3(Q147L) complex

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