7JVP: SKF-83959-bound dopamine receptor 1

Cryo-EM structure of SKF-83959-bound dopamine receptor 1 in complex with Gs protein. Determined by electron microscopy at 2.9 Å resolution. Released 24 Feb 2021.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, synthetic construct
Chains: 5
Atoms: 8,486
Mol. weight: 166.57 kDa
Ligands: PLM, CLR, SK9
Released: 24 Feb 2021

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

Secondary structure: helices and β-sheets

7JVP contains 34 α-helices and 47 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: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-39	30
β-strand	41-47	7	2
α-helix	53-61	9
β-strand	207-213	7	2
β-strand	218-224	7	2
α-helix	232-235	4
α-helix	236-240	5
β-strand	243-249	7	2
α-helix	265-278	14
α-helix	281-283	3
α-helix	285	1
β-strand	286-292	7	2
α-helix	294-303	10
α-helix	308-311	4
α-helix	313-316	4
α-helix	332-352	21
β-strand	359-363	5	2
α-helix	371-390	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	34-36	3
β-strand	46-51	6	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
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
α-helix	145	1
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	249-254	6	8
β-strand	259-265	7	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-308	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-340	5	3

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-23	17
α-helix	30-43	14

Chain N: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	18-25	8	10
β-strand	34-39	6	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	68-73	6	10
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-98	7	11
β-strand	118	1	11
β-strand	122-126	5	11

Chain R: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-50	30
α-helix	52-56	5
α-helix	59-72	14
α-helix	73-77	5
α-helix	78-87	10
α-helix	95-126	32
α-helix	128-134	7
α-helix	137-160	24
β-strand	165	1	1
α-helix	166-167	2
β-strand	190	1	1
α-helix	192-199	8
α-helix	200-204	5
α-helix	205-238	34
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	R	protein	502	Homo sapiens	P21728 (AlphaFold model)
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	393	Homo sapiens	P63092 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	354	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	67	Homo sapiens	P59768 (AlphaFold model)
nanobody 35	N	protein	135	synthetic construct

Sequence of entity 1 (R), FASTA

>7JVP_1 D(1A) dopamine receptor (chains R)
DYKDDDDVDMGQPGNGSAFLLAPNGSHAPDHDVTQQRDEENLYFQGASMRTLNTSAMDGT
GLVVERDFSVRILTACFLSLLILSTLLGNTLVCAAVIRFRHLRSKVTNFFVISLAVSDLL
VAVLVMPWKAVAEIAGFWPFGSFCNIWVAFDIMCSTASILNLCVISVDRYWAISSPFRYE
RKMTPKAAFILISVAWTLSVLISFIPVQLSWHKAKPTSPSDGNATSLAETIDNCDSSLSR
TYAISSSVISFYIPVAIMIVTYTRIYRIAQKQIRRIAALERAAVHAKNCQTTTGNGKPVE
CSQPESSFKMSFKRETKVLKTLSVIMGVFVCCWLPFFILNCILPFCGSGETQPFCIDSNT
FDVFVWFGWANSSLNPIIYAFNADFRKAFSTLLGCYRLCPATNNAIETVSINNNGAAMFS
SHHEPRGSISKECNLVYLIPHAVGSSEDLKKEEAAGIARPLEKLSPALSVILDYDTDVSL
EKIQPITQNGQHPTHHHHHHHH

Sequence of entity 2 (A), FASTA

>7JVP_2 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
GCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKSTIVKQMR
ILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELAN
PENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLDK
IDVIKQADYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDV
TAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKV
LAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYP
HFTCSVDTENIRRVFNDCRDIIQRMHLRQYELL

Sequence of entity 3 (B), FASTA

>7JVP_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
HHHHHHHHMGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRT
RRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAP
SGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCA
LWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHES
DINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLA
GYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNG

Sequence of entity 4 (G), FASTA

>7JVP_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Sequence of entity 5 (N), FASTA

>7JVP_5 nanobody 35 (chains N)
MQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASIS
YTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRG
QGTQVTVSSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	5
CLR	Cholesterol	C27 H46 O	6
SK9	(1R)-6-chloro-3-methyl-1-(3-methylphenyl)-2,3,4,5-tetrahydro-1H-3-benzazepine-7…	C18 H20 Cl N O2	1

Primary citation

Structural insights into the human D1 and D2 dopamine receptor signaling complexes. Zhuang, Y., Xu, P., Mao, C. et al. Cell (2021) 184:931-942.e18. DOI 10.1016/j.cell.2021.01.027 · 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
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…
7JV5 3.0 Å, Cryo-EM structure of SKF-81297-bound dopamine receptor 1 in complex with Gs protein

Browse structure collections

About this viewer

MolViewer shows 7JVP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.