7LJD: D dopamine receptor

Allosteric modulator LY3154207 binding to dopamine-bound dopamine receptor 1 in complex with miniGs protein. Determined by electron microscopy at 3.2 Å resolution. Released 3 Mar 2021.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Rattus norvegicus, Bos taurus
Chains: 5
Atoms: 8,518
Mol. weight: 149.55 kDa
Ligands: PLM, CLR, G4C, LDP
Released: 3 Mar 2021

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

Secondary structure: helices and β-sheets

7LJD contains 29 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	10-39	30
β-strand	41-47	7	1
β-strand	64-65	2	1
β-strand	69-75	7	1
β-strand	80-86	7	1
α-helix	96-102	7
β-strand	105-111	7	1
α-helix	118-130	13
β-strand	138-144	7	1
α-helix	146-153	8
α-helix	159-163	5
α-helix	165-168	4
α-helix	184-204	21
β-strand	211-214	4	1
α-helix	223-242	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	47-51	5	2
β-strand	58-62	5	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
α-helix	145	1
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	176-180	5	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	260-264	5	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	336-339	4	2

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-23	16
α-helix	30-43	14

Chain N: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	17-25	9	9
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	60	1	10
α-helix	62-64	3
β-strand	68-73	6	9
β-strand	78-84	7	9
β-strand	92-98	7	10
β-strand	118	1	10
β-strand	122-126	5	10

Chain R: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	22-49	28
α-helix	53-56	4
α-helix	60-72	13
α-helix	73-77	5
α-helix	78-87	10
α-helix	95-126	32
α-helix	128-134	7
α-helix	137-161	25
α-helix	192-199	8
α-helix	200-204	5
α-helix	205-241	37
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 Gs protein 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)
Nanobody 35	N	protein	135	Lama glama

Sequence of entity 1 (R), FASTA

>7LJD_1 D(1A) dopamine receptor (chains R)
DYKDDDDVDMGQPGNGSAFLLAPNGSHAPDHDVTQQRDEENLYFQGASMRTLNTSAMDGT
GLVVERDFSVRILTACFLSLLILSTLLGNTLVCAAVIRFRHLRSKVTNFFVISLAVSDLL
VAVLVMPWKAVAEIAGFWPFGSFCNIWVAFDIMCSTASILNLCVISVDRYWAISSPFRYE
RKMTPKAAFILISVAWTLSVLISFIPVQLSWHKAKPTSPSDGNATSLAETIDNCDSSLSR
TYAISSSVISFYIPVAIMIVTYTRIYRIAQKQIRRIAALERAAVHAKNCQTTTGNGKPVE
CSQPESSFKMSFKRETKVLKTLSVIMGVFVCCWLPFFILNCILPFCGSGETQPFCIDSNT
FDVFVWFGWANSSLNPIIYAFNADFRKAFSTLLGCYRLCPATNNAIETVSINNNGAAMFS
SHHEPRGSISKECNLVYLIPHAVGSSEDLKKEEAAGIARPLEKLSPALSVILDYDTDVSL
EKIQPITQNGQHPTHHHHHHHH

Sequence of entity 2 (A), FASTA

>7LJD_2 Engineered Gs protein alpha subunit (chains A)
MGCLGNSKTEDQRNEEKAQREANKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQM
RIYHVNSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNKWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDCRDIIQRMHL
RQYELL

Sequence of entity 3 (B), FASTA

>7LJD_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

>7LJD_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Sequence of entity 5 (N), FASTA

>7LJD_5 Nanobody 35 (chains N)
MQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASIS
YTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRG
QGTQVTVSSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	4
CLR	Cholesterol	C27 H46 O	5
G4C	2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-…	C24 H29 Cl2 N O3	1
LDP	L-dopamine	C8 H11 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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