7X2F: D dopamine receptor

Cryo-EM structure of the dopamine and LY3154207-bound D1 dopamine receptor and mini-Gs complex. Determined by electron microscopy at 3.0 Å resolution. Released 15 Jun 2022.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 5
Atoms: 8,249
Mol. weight: 147.31 kDa
Ligands: LDP, G4C, CLR
Released: 15 Jun 2022

Explore 7X2F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7X2F contains 34 α-helices and 46 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	13-38	26
β-strand	40-46	7	1
α-helix	53-59	7
β-strand	209-214	6	1
β-strand	217-223	7	1
α-helix	233-238	6
β-strand	243-249	7	1
α-helix	265-277	13
β-strand	286-292	7	1
α-helix	294-303	10
α-helix	308-311	4
α-helix	313-317	5
α-helix	326-327	2
α-helix	332-352	21
β-strand	359-363	5	1
α-helix	371-390	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-52	6	5
β-strand	58-63	6	6
β-strand	69-74	6	6
β-strand	78-83	6	6
β-strand	88-94	7	6
β-strand	100-105	6	7
β-strand	111-116	6	7
β-strand	121-125	5	7
β-strand	135-139	5	7
β-strand	146-151	6	8
β-strand	156-161	6	8
β-strand	165-170	6	8
β-strand	175-181	7	8
β-strand	187-192	6	9
β-strand	198-203	6	9
β-strand	208-212	5	9
β-strand	218-222	5	9
β-strand	229-234	6	10
β-strand	240-245	6	10
β-strand	250-254	5	10
β-strand	259-264	6	10
β-strand	273-278	6	11
β-strand	284-289	6	11
β-strand	294-298	5	11
β-strand	304-308	5	11
β-strand	315-320	6	5
β-strand	327-331	5	5
β-strand	335-339	5	5

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain E: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	2
β-strand	11-12	2	3
β-strand	18-25	8	2
α-helix	29-31	3
β-strand	34-39	6	4
β-strand	45-51	7	4
β-strand	58-60	3	4
β-strand	69-73	5	2
β-strand	78-83	6	2
α-helix	88-90	3
β-strand	92-98	7	4
β-strand	118	1	4
β-strand	122-124	3	4
β-strand	125-126	2	3

Chain F: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	22-50	29
α-helix	52-56	5
α-helix	60-76	17
α-helix	78-87	10
α-helix	95-125	31
α-helix	128-134	7
α-helix	137-160	24
α-helix	189-191	3
α-helix	192-199	8
α-helix	200-204	5
α-helix	205-240	36
α-helix	265-298	34
α-helix	310-331	22
α-helix	335-345	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
D(1A) dopamine receptor	F	protein	473	Homo sapiens	P21728 (AlphaFold model)
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Isoform Gnas-2 of Guanine…	A	protein	248	Homo sapiens	P63092 (AlphaFold model)
Nanobody35	E	protein	160	synthetic construct
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	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)

Sequence of entity 1 (F), FASTA

>7X2F_1 D(1A) dopamine receptor (chains F)
MKTIIALSYIFCLVFADYKDDDDASIDMRTLNTSAMDGTGLVVERDFSVRILTACFLSLL
ILSTLLGNTLVCAAVIRFRHLRSKVTNFFVISLAVSDLLVAVLVMPWKAVAEIAGFWPFG
SFCNIWVAFDIMCSTASILNLCVISVDRYWAISSPFRYERKMTPKAAFILISVAWTLSVL
ISFIPVQLSWHKAKPTSPSDGNATSLAETIDNCDSSLSRTYAISSSVISFYIPVAIMIVT
YTRIYRIAQKQIRRIAALERAAVHAKNCQTTTGNGKPVECSQPESSFKMSFKRETKVLKT
LSVIMGVFVCCWLPFFILNCILPFCGSGETQPFCIDSNTFDVFVWFGWANSSLNPIIYAF
NADFRKAFSTLLGCYRLCPATNNAIETVSINNNGAAMFSSHHEPRGSISKECNLVYLIPH
AVGSSEDLKKEEAAGIARPLEKLSPALSVILDYDTDVSLEKIQPITQNGQHPT

Sequence of entity 2 (A), FASTA

>7X2F_2 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
NSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRILHG
GSGGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRL
QEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATP
EPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENARRIFNDCRDIIQRM
HLRQYELL

Sequence of entity 3 (E), FASTA

>7X2F_3 Nanobody35 (chains E)
MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVR
QAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAR
CPAPFTRDCFDVTSTTYAYRGQGTQVTVSSHHHHHHEPEA

Sequence of entity 4 (B), FASTA

>7X2F_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (D), FASTA

>7X2F_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFSAIL

Ligands and cofactors

ID	Name	Formula	Copies
LDP	L-dopamine	C8 H11 N O2	1
G4C	2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-…	C24 H29 Cl2 N O3	1
CLR	Cholesterol	C27 H46 O	2

Primary citation

Ligand recognition and biased agonism of the D1 dopamine receptor. Teng, X., Chen, S., Nie, Y. et al. Nat Commun (2022) 13:3186-3186. DOI 10.1038/s41467-022-30929-w · PubMed

Other PDB entries of the same protein (UniProt P21728 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9WG6 2.44 Å, D1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815
9WG0 2.59 Å, D1R-Gs in complexed with SKF81297/LY3154207/BMSA1/UNC10062
9LLJ 2.61 Å, Cryo-EM structure of D1R-Gs in complex with de novo designed GEM targetingTM1/2/4 and…
9LLF 2.64 Å, Cryo-EM structure of D1R-Gs in complex with de novo designed GEM targeting TM3/4/5
9WEU 2.65 Å, D1R-Gs in complexed with SKF81297/LY3154207/BMSA1
9I54 2.72 Å, Dopamine 1 receptor:GaS complex bound to 24
9LLH 2.73 Å, Cryo-EM structure of D1R-Gs in complex with de novo designed agonist-positive allosteric…
9LLG 2.77 Å, Cryo-EM structure of D1R in complex with de novo designed negative allosteric GEM…
9I52 2.8 Å, Dopamine 1 receptor:GaS complex bound to 19B
7JVP 2.9 Å, Cryo-EM structure of SKF-83959-bound dopamine receptor 1 in complex with Gs protein
9LLE 2.9 Å, Cryo-EM structure of D1R-Gs in complex with de novo designed GEM targeting TM1/2/4
9LWC 2.9 Å, Cryo-EM structure of epinephrine bound dopamine receptor 1…

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