9VNF: 5-HT1AR-GoA

Cryo-EM structure of 5-HT1AR-GoA in complex with (S)-pindolol. Determined by electron microscopy at 2.74 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 2.74 Å
Organisms: Homo sapiens, Mus musculus, Escherichia coli
Chains: 5
Atoms: 8,697
Mol. weight: 176.94 kDa
Ligands: T7M, CLR, A1ES4
Released: 12 Nov 2025

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

Secondary structure: helices and β-sheets

9VNF contains 42 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 B: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-40	8	1
α-helix	46-53	8
β-strand	186-192	7	1
β-strand	195-201	7	1
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-227	7	1
α-helix	243-255	13
β-strand	264-270	7	1
α-helix	272-281	10
α-helix	297-309	13
β-strand	319-323	5	1
α-helix	331-350	20

Chain C: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	30-33	4
α-helix	38-40	3
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	88-94	7	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
α-helix	186	1
β-strand	187-192	6	6
β-strand	198-203	6	6
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	317-320	4	2
β-strand	327-330	4	2
β-strand	336-339	4	2

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	27-29	3
α-helix	30-43	14
α-helix	53-55	3

Chain E: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	18-25	8	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	65	1	9
β-strand	68-73	6	9
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
α-helix	125-127	3
β-strand	128-129	2	11
β-strand	135-136	2	12
β-strand	143-149	7	11
β-strand	154	1	13
β-strand	160	1	13
β-strand	162-167	6	12
β-strand	175-177	3	12
β-strand	183	1	12
α-helix	184	1
β-strand	191-196	6	11
β-strand	199-204	6	11
α-helix	209-211	3
β-strand	213-219	7	12
α-helix	227-230	4
β-strand	231-234	4	12

Chain R: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	35-63	29
α-helix	65-67	3
α-helix	70-84	15
α-helix	85-89	5
α-helix	90-99	10
α-helix	106-139	34
α-helix	141-146	6
α-helix	150-168	19
α-helix	170-174	5
α-helix	193-200	8
α-helix	201-205	5
α-helix	206-229	24
α-helix	330-347	18
α-helix	348-352	5
α-helix	353-367	15
α-helix	368-371	4
α-helix	381-397	17
α-helix	398-402	5
α-helix	405-412	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(o) subunit alpha	B	protein	354	Homo sapiens	P09471 (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

>9VNF_1 Guanine nucleotide-binding protein G(o) subunit alpha (chains B)
MGSTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGAGESGKNTIVKQMKIIHEDG
FSGEDVKQYKPVVYSNTIQSLAAIVRAMDTLGIEYGDKERKADAKMVCDVVSRMEDTEPF
SAELLSAMMRLWGDSGIQECFNRSREYQLNDSAKYYLDSLDRIGAADYQPTEQDILRTRV
KTTGIVETHFTFKNLHFRLFDVGAQRSERKKWIHCFEDVTAIIFCVALSGYDQVLHEDET
TNRMHASLKLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGPNTYEDA
AAYIQAQFESKNRSPNKEIYCHMTCSTDTNNIQVVFDAVTDIIIANNLRGCGLY

Sequence of entity 2 (C), FASTA

>9VNF_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

>9VNF_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (E), FASTA

>9VNF_4 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAA

Sequence of entity 5 (R), FASTA

>9VNF_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
T7M	(2R)-1-(heptadecanoyloxy)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahyd…	C46 H82 O16 P2	1
CLR	Cholesterol	C27 H46 O	2
A1ES4	(2~{S})-1-(1~{H}-indol-4-yloxy)-3-(propan-2-ylamino)propan-2-ol	C14 H20 N2 O2	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 P09471 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BSB 2.32 Å, Global reconstruction of DRD2 bound to LSD in complex with a mini-GoA and scFv16…
9VJE 2.47 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with buspirone
9K20 2.65 Å, Cryo-EM structure of ATP-bound P2Y purinoceptor 2-miniGo-scFv16 complex
9VJ5 2.69 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with gepirone
8E9X 2.7 Å, CryoEM structure of miniGo-coupled hM4Di in complex with DCZ
9T88 2.74 Å, Cryo-EM structure of ESG-2-37-bound D3 dopamine receptor with mini-Go
8YN7 2.77 Å, Cryo-EM structure of histamine H3 receptor in complex with immethridine and miniGo
8YN8 2.77 Å, Cryo-EM structure of histamine H3 receptor in complex with proxyfan and miniGo
9KVP 2.79 Å, Structure of SB290157 bound to human C3aR in complex with Go (Full map)
7W2Z 2.8 Å, Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go complex
8XXH 2.8 Å, Structure of CXCR2 bound to CXCL2 (CXCR2-CXCL2-Go Full map)
9PLO 2.8 Å, Structure of alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and…

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