9F33: Dopamine 3 Receptor:Go complex

Cryo-EM structure of Dopamine 3 Receptor:Go complex bound to bitopic FOB02-04A - Conformation A. Determined by electron microscopy at 3.05 Å resolution. Released 18 Sept 2024.

Method: Electron microscopy
Resolution: 3.05 Å
Organisms: Homo sapiens, Rattus norvegicus, Mus musculus
Chains: 5
Atoms: 8,666
Mol. weight: 191.43 kDa
Ligands: A1H9N
Released: 18 Sept 2024

Explore 9F33 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F33 contains 36 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: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-38	5	1
α-helix	46-53	8
β-strand	186-191	6	1
β-strand	196-201	6	1
α-helix	210-213	4
α-helix	214-216	3
β-strand	221-227	7	1
α-helix	243-255	13
β-strand	264-270	7	1
α-helix	272-281	10
α-helix	284-286	3
α-helix	297-309	13
β-strand	319	1	1
β-strand	322-323	2	1
α-helix	331-351	21

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	5-25	21
α-helix	30-33	4
α-helix	38-42	5
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	120-125	6	4
β-strand	134-140	7	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	175-181	7	5
α-helix	186	1
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	217-223	7	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	2
β-strand	327-331	5	2
β-strand	335-339	5	2

Chain C: 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	56-58	3

Chain E: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	18-25	8	9
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	65	1	9
β-strand	68-73	6	9
β-strand	78-83	6	9
β-strand	92-99	8	11
β-strand	110-111	2	11
β-strand	115-117	3	11
β-strand	118-119	2	10
β-strand	140-141	2	12
β-strand	146-148	3	13
β-strand	151	1	14
β-strand	153	1	14
β-strand	155-161	7	12
β-strand	166-167	2	15
β-strand	171-172	2	15
β-strand	174-179	6	13
β-strand	186-190	5	13
β-strand	194-195	2	13
α-helix	196	1
β-strand	203-208	6	12
β-strand	211-216	6	12
α-helix	221-223	3
β-strand	225-231	7	13
α-helix	237	1
β-strand	243-246	4	13

Chain R: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	30-56	27
α-helix	63-77	15
α-helix	78-82	5
α-helix	83-91	9
α-helix	100-133	34
α-helix	135-138	4
α-helix	143-167	25
α-helix	168-172	5
α-helix	186-193	8
α-helix	194-198	5
α-helix	199-222	24
α-helix	324-353	30
α-helix	362-383	22
α-helix	388-397	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(o) subunit alpha	A	protein	354	Homo sapiens	P09471 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	355	Rattus norvegicus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
Antibody scFv16	E	protein	270	Mus musculus
Green fluorescent protein,D(3) dopamine receptor	R	protein	669	Aequorea victoria, Homo sapiens	P35462 (AlphaFold model), P42212

Sequence of entity 1 (A), FASTA

>9F33_1 Guanine nucleotide-binding protein G(o) subunit alpha (chains A)
MGCTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGAGESGKNTIVKQMKIIHEDG
FSGEDVKQYKPVVYSNTIQSLAAIVRAMDTLGIEYGDKERKADAKMVCDVVSRMEDTEPF
SAELLSAMMRLWGDSGIQECFNRSREYQLNDSAKYYLDSLDRIGAADYQPTEQDILRTRV
KTTGIVETHFTFKNLHFRLFDVGAQRSERKKWIHCFEDVTAIIFCVALSGYDQVLHEDET
TNRMHASLKLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGPNTYEDA
AAYIQAQFESKNRSPNKEIYCHMTCSTDTNNIQVVFDAVTDIIIANNLRGCGLY

Sequence of entity 2 (B), FASTA

>9F33_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHHHENLYFQGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQM
RTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAY
APSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTT
CALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGH
ESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLL
LAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>9F33_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFSAIL

Sequence of entity 4 (E), FASTA

>9F33_4 Antibody scFv16 (chains E)
MDVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIY
YADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTV
SSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLELKGSLEVLFQGPAAAHHHHHHHH

Sequence of entity 5 (R), FASTA

>9F33_5 Green fluorescent protein,D(3) dopamine receptor (chains R)
MKTIIALSYIFCLVFADYKDDDDKVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGD
ATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQER
TIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADK
QKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRD
HMVLLEFVTAAGITLGMDELYKLEVLFQGPASLSQLSSHLNYTCGAENSTGASQARPHAY
YALSYCALILAIVFGNGLVCMAVLKERALQTTTNYLVVSLAVADLLVATLVMPWVVYLEV
TGGVWNFSRICCDVFVTLDVMMCTASIWNLCAISIDRYTAVVMPVHYQHGTGQSSCRRVA
LMITAVWVLAFAVSCPLLFGFNTTGDPTVCSISNPDFVIYSSVVSFYLPFGVTVLVYARI
YVVLKQRRRKRILTRQNSQCNSVRPGFPQQTLSPDPAHLELKRYYSICQDTALGGPGFQE
RGGELKREEKTRNSLSPTIAPKLSLEVRKLSNGRLSTSLKLGPLQPRGVPLREKKATQMV
AIVLGAFIVCWLPFFLTHVLNTHCQTCHVSPELYSATTWLGYVNSALNPVIYTTFNIEFR
KAFLKILSC

Ligands and cofactors

ID	Name	Formula	Copies
A1H9N	N-[2-[(1R,2S)-2-[[(2S,5S)-2-(6-azanylpyridin-3-yl)-5-methyl-morpholin-4-yl]meth…	C25 H31 N5 O2	1

Primary citation

A bitopic agonist bound to the dopamine 3 receptor reveals a selectivity site. Arroyo-Urea, S., Nazarova, A.L., Carrion-Antoli, A. et al. Nat Commun (2024) 15:7759-7759. DOI 10.1038/s41467-024-51993-4 · 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
9VNF 2.74 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with (S)-pindolol
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)

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