7LJC: D dopamine receptor

Allosteric modulator LY3154207 binding to SKF-81297-bound dopamine receptor 1 in complex with miniGs protein. Determined by electron microscopy at 3.0 Å resolution. Released 3 Mar 2021.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Rattus norvegicus, Bos taurus
Chains: 5
Atoms: 8,544
Mol. weight: 150.61 kDa
Ligands: PLM, CLR, G4C, SK0
Released: 3 Mar 2021

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

Secondary structure: helices and β-sheets

7LJC contains 32 α-helices and 48 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	10-39	30
β-strand	41-47	7	2
α-helix	53-55	3
β-strand	62-65	4	2
β-strand	70-75	6	2
β-strand	80-85	6	2
α-helix	96-102	7
β-strand	105-111	7	2
α-helix	118-129	12
β-strand	138-144	7	2
α-helix	146-155	10
α-helix	160-163	4
α-helix	165-167	3
α-helix	184-204	21
β-strand	211-215	5	2
α-helix	223-242	20

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
β-strand	47-51	5	3
β-strand	58-62	5	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	89-94	6	4
β-strand	103-105	3	5
β-strand	111-114	4	5
β-strand	121-125	5	5
β-strand	135-139	5	5
β-strand	148-151	4	6
β-strand	156-160	5	6
β-strand	166-170	5	6
β-strand	176-180	5	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	303-307	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	30-43	14
α-helix	53-55	3

Chain N: 2 helices, 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
α-helix	29-31	3
β-strand	34-39	6	11
β-strand	45-51	7	11
β-strand	58-60	3	11
α-helix	62-64	3
β-strand	68-73	6	10
β-strand	78-83	6	10
β-strand	92-98	7	11
β-strand	118	1	11
β-strand	122-126	5	11

Chain R: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	22-50	29
α-helix	52-55	4
α-helix	60-76	17
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
α-helix	189	1
β-strand	190	1	1
α-helix	191	1
α-helix	192-199	8
α-helix	200-204	5
α-helix	205-239	35
α-helix	265-297	33
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)
Engineered human Gs alpha subunit	A	protein	246	Homo sapiens	P63092 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	353	Rattus norvegicus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	67	Bos taurus	P63212 (AlphaFold model)
Nanoboy 35	N	protein	135	Lama glama

Sequence of entity 1 (R), FASTA

>7LJC_1 D(1A) dopamine receptor (chains R)
DYKDDDDVDMGQPGNGSAFLLAPNGSHAPDHDVTQQRDEENLYFQGASMRTLNTSAMDGT
GLVVERDFSVRILTACFLSLLILSTLLGNTLVCAAVIRFRHLRSKVTNFFVISLAVSDLL
VAVLVMPWKAVAEIAGFWPFGSFCNIWVAFDIMCSTASILNLCVISVDRYWAISSPFRYE
RKMTPKAAFILISVAWTLSVLISFIPVQLSWHKAKPTSPSDGNATSLAETIDNCDSSLSR
TYAISSSVISFYIPVAIMIVTYTRIYRIAQKQIRRIAALERAAVHAKNCQTTTGNGKPVE
CSQPESSFKMSFKRETKVLKTLSVIMGVFVCCWLPFFILNCILPFCGSGETQPFCIDSNT
FDVFVWFGWANSSLNPIIYAFNADFRKAFSTLLGCYRLCPATNNAIETVSINNNGAAMFS
SHHEPRGSISKECNLVYLIPHAVGSSEDLKKEEAAGIARPLEKLSPALSVILDYDTDVSL
EKIQPITQNGQHPTHHHHHHHH

Sequence of entity 2 (A), FASTA

>7LJC_2 Engineered human Gs alpha subunit (chains A)
MGCLGNSKTEDQRNEEKAQREANKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQM
RIYHVNSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDCRDIIQRMHL
RQYELL

Sequence of entity 3 (B), FASTA

>7LJC_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
HHHHHHHHMGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRT
RRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAP
SGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCA
LWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHES
DINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLA
GYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G), FASTA

>7LJC_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Sequence of entity 5 (N), FASTA

>7LJC_5 Nanoboy 35 (chains N)
MQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASIS
YTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRG
QGTQVTVSSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	6
CLR	Cholesterol	C27 H46 O	6
G4C	2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-…	C24 H29 Cl2 N O3	1
SK0	(1R)-6-chloro-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol	C16 H16 Cl N O2	1

Primary citation

Mechanism of dopamine binding and allosteric modulation of the human D1 dopamine receptor. Zhuang, Y., Krumm, B., Zhang, H. et al. Cell Res (2021) 31:593-596. DOI 10.1038/s41422-021-00482-0 · 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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