9F34: Dopamine 3 receptor:Go complex
Cryo-EM structure of Dopamine 3 receptor:Go complex bound to bitopic FOB02-04A - Conformation B. Determined by electron microscopy at 3.09 Å resolution. Released 18 Sept 2024.
- Method
- Electron microscopy
- Resolution
- 3.09 Å
- Organisms
- Homo sapiens, Rattus norvegicus, Mus musculus
- Chains
- 5
- Atoms
- 8,633
- Mol. weight
- 190.11 kDa
- Ligands
- A1H9N
- Released
- 18 Sept 2024
Explore 9F34 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9F34 contains 38 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, 9 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 | 221-223 | 3 | 1 |
| β-strand | 225-227 | 3 | 2 |
| α-helix | 243-255 | 13 | |
| β-strand | 264-265 | 2 | 1 |
| β-strand | 268-270 | 3 | 2 |
| 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 | 2 |
| α-helix | 331-351 | 21 | |
Chain B: 5 helices, 30 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-25 | 21 | |
| α-helix | 30-33 | 4 | |
| α-helix | 38-43 | 6 | |
| 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 | 88-94 | 7 | 4 |
| α-helix | 95 | 1 | |
| β-strand | 100-105 | 6 | 5 |
| β-strand | 111-116 | 6 | 5 |
| β-strand | 120-125 | 6 | 5 |
| β-strand | 134-140 | 7 | 5 |
| β-strand | 146-151 | 6 | 6 |
| β-strand | 156-161 | 6 | 6 |
| β-strand | 165-170 | 6 | 6 |
| β-strand | 175-181 | 7 | 6 |
| β-strand | 187 | 1 | 7 |
| β-strand | 191-192 | 2 | 8 |
| β-strand | 198-202 | 5 | 8 |
| β-strand | 203 | 1 | 7 |
| β-strand | 207-212 | 6 | 8 |
| β-strand | 217-223 | 7 | 8 |
| β-strand | 229-234 | 6 | 9 |
| β-strand | 240-245 | 6 | 9 |
| β-strand | 250-254 | 5 | 9 |
| β-strand | 259-264 | 6 | 9 |
| α-helix | 272 | 1 | |
| β-strand | 273-278 | 6 | 10 |
| β-strand | 284-289 | 6 | 10 |
| β-strand | 293-298 | 6 | 10 |
| β-strand | 304-309 | 6 | 10 |
| β-strand | 315-320 | 6 | 3 |
| β-strand | 327-331 | 5 | 3 |
| β-strand | 336-339 | 4 | 3 |
Chain C: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-23 | 15 | |
| α-helix | 30-43 | 14 | |
| α-helix | 45-47 | 3 | |
| α-helix | 56-58 | 3 | |
Chain E: 4 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 11 |
| β-strand | 10-12 | 3 | 12 |
| β-strand | 18-25 | 8 | 11 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-39 | 7 | 12 |
| β-strand | 45-51 | 7 | 12 |
| β-strand | 58-60 | 3 | 12 |
| β-strand | 68-73 | 6 | 11 |
| β-strand | 78-83 | 6 | 11 |
| β-strand | 92-99 | 8 | 12 |
| β-strand | 111 | 1 | 12 |
| β-strand | 115-119 | 5 | 12 |
| β-strand | 141 | 1 | 13 |
| β-strand | 146-148 | 3 | 14 |
| β-strand | 155-160 | 6 | 13 |
| β-strand | 166 | 1 | 15 |
| β-strand | 172 | 1 | 15 |
| β-strand | 174-179 | 6 | 14 |
| β-strand | 186-190 | 5 | 14 |
| β-strand | 194-195 | 2 | 14 |
| α-helix | 196 | 1 | |
| β-strand | 203-208 | 6 | 13 |
| β-strand | 211-216 | 6 | 13 |
| α-helix | 221-223 | 3 | |
| β-strand | 225-231 | 7 | 14 |
| α-helix | 237 | 1 | |
| β-strand | 243-246 | 4 | 14 |
Chain R: 16 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-56 | 24 | |
| 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 | 144-167 | 24 | |
| α-helix | 168-172 | 5 | |
| α-helix | 186-193 | 8 | |
| α-helix | 194-198 | 5 | |
| α-helix | 199-222 | 24 | |
| α-helix | 324-340 | 17 | |
| α-helix | 343-353 | 11 | |
| α-helix | 362-380 | 19 | |
| α-helix | 381-385 | 5 | |
| 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 | 259 | Mus musculus | |
| Green fluorescent protein,D(3) dopamine receptor | R | protein | 669 | Homo sapiens | P35462 (AlphaFold model), P42212 |
Sequence of entity 1 (A), FASTA
>9F34_1 Guanine nucleotide-binding protein G(o) subunit alpha (chains A)
MGCTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGAGESGKNTIVKQMKIIHEDG
FSGEDVKQYKPVVYSNTIQSLAAIVRAMDTLGIEYGDKERKADAKMVCDVVSRMEDTEPF
SAELLSAMMRLWGDSGIQECFNRSREYQLNDSAKYYLDSLDRIGAADYQPTEQDILRTRV
KTTGIVETHFTFKNLHFRLFDVGAQRSERKKWIHCFEDVTAIIFCVALSGYDQVLHEDET
TNRMHASLKLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGPNTYEDA
AAYIQAQFESKNRSPNKEIYCHMTCSTDTNNIQVVFDAVTDIIIANNLRGCGLY
Sequence of entity 2 (B), FASTA
>9F34_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
>9F34_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFSAIL
Sequence of entity 4 (E), FASTA
>9F34_4 Antibody scFv16 (chains E)
MDVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIY
YADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTV
SSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLELKGSLEVLFQGP
Sequence of entity 5 (R), FASTA
>9F34_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)
Browse structure collections
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