8JXS: Nanobody-bound DRD1_PF-6142 complex

Structure of nanobody-bound DRD1_PF-6142 complex. Determined by electron microscopy at 3.0 Å resolution. Released 4 Sept 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Escherichia coli K-12, Staphylococcus aureus
Chains: 5
Atoms: 8,596
Mol. weight: 167.33 kDa
Ligands: V6X
Released: 4 Sept 2024

Explore 8JXS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JXS contains 44 α-helices and 69 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: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	23-50	28
α-helix	60-72	13
α-helix	73-77	5
α-helix	78-87	10
α-helix	96-126	31
α-helix	128-134	7
α-helix	137-160	24
α-helix	188-191	4
α-helix	192-199	8
α-helix	200-204	5
α-helix	205-235	31
α-helix	266-297	32
α-helix	310-331	22
α-helix	335-344	10

Chain B: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-13	3	2
β-strand	18-25	8	1
β-strand	32-39	8	3
β-strand	46-52	7	3
β-strand	57-59	3	3
β-strand	64	1	1
β-strand	67-71	5	1
β-strand	78-82	5	1
α-helix	87-89	3
β-strand	91-99	9	3
β-strand	107-110	4	3
β-strand	114-116	3	3
β-strand	117-119	3	2

Chain C: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	44-51	8
β-strand	63-64	2	4
α-helix	65-74	10
α-helix	84-89	6
α-helix	92-98	7
β-strand	99-100	2	5
β-strand	103-104	2	5
β-strand	108-112	5	4
β-strand	115-118	4	6
β-strand	129	1	7
α-helix	130-132	3
α-helix	133-140	8
α-helix	155-164	10
β-strand	172-173	2	8
β-strand	176-177	2	8
α-helix	187-201	15
α-helix	211-219	9
β-strand	225-228	4	6
α-helix	230-232	3
β-strand	244-246	3	6
α-helix	247-249	3
β-strand	250	1	7
β-strand	251	1	9
β-strand	254	1	9
α-helix	255-256	2
α-helix	258	1
β-strand	259-260	2	10
β-strand	261-264	4	4
α-helix	316-326	11
β-strand	329-330	2	10
α-helix	331-332	2
α-helix	337-351	15
α-helix	358-369	12
α-helix	375-386	12
α-helix	392-405	14
β-strand	485-488	4	11
β-strand	493-496	4	11
α-helix	504-517	14
β-strand	532-535	4	11

Chain H: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	11-12	2	13
β-strand	18-25	8	12
β-strand	33-39	7	14
β-strand	46-51	6	14
β-strand	58-60	3	14
β-strand	65	1	12
β-strand	68-73	6	12
α-helix	74-76	3
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-99	8	14
α-helix	103-106	4
β-strand	113	1	14
β-strand	117-119	3	14
β-strand	120-121	2	13
α-helix	125-126	2
β-strand	130-134	5	15
β-strand	148-155	8	15
β-strand	160-164	5	11
β-strand	173-180	8	15
β-strand	186-192	7	15
β-strand	206-210	5	11
β-strand	215-218	4	11

Chain L: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	16
β-strand	10-14	5	17
β-strand	19-25	7	16
β-strand	30	1	18
β-strand	37	1	18
β-strand	39-44	6	17
β-strand	50-55	6	17
β-strand	59-60	2	17
α-helix	61	1
β-strand	68-73	6	16
β-strand	76-81	6	16
α-helix	86-88	3
β-strand	91-96	6	17
β-strand	102-103	2	17
β-strand	107-112	6	17
α-helix	116-118	3
β-strand	119-123	5	19
α-helix	124-126	3
α-helix	127-132	6
β-strand	138-144	7	19
β-strand	165-168	4	19
β-strand	178-183	6	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
D(1A) dopamine receptor	A	protein	352	Homo sapiens	P21728 (AlphaFold model)
NBA3	B	protein	125	Homo sapiens
Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin…	C	protein	559	Escherichia coli K-12, Staphylococcus aureus	P06654 (AlphaFold model), P0A015 (AlphaFold model), P0AEX9 (AlphaFold model), P38507
Fab 8D3 heavy chain	H	protein	253	Mus musculus
Fab 8D3 light chain	L	protein	239	Mus musculus

Sequence of entity 1 (A), FASTA

>8JXS_1 D(1A) dopamine receptor (chains A)
GTGLVVERDFSVRILTACFLSLLILSTLLGNTLVCAAVIRFRHLRSKVTNFFVISLAVSD
LLVAVLVMPWKAVAEIAGFWPFGSFCNIWVAFDIMCSTASIWNLCVISVDRYWAISSPFR
YERKMTPKAAFILISVAWTLSVLISFIPVQLSWHKAKPTSPSDGNATSLAETIDNCDSSL
SRTYAISSSVISFYIPVAIMIVTYTRIYRIAQKQIRRIAALERAAVHAKNCQTTTGNGKP
VECSQPESSFKMSFKRETKVLKTLSVIMGVFVCCWLPFFILNCILPFCGSGETQPFCIDS
NTFDVFVWFGWANSALNPIIYAFNADFRKAFSTLLGCYRLCPATNNAIETVS

Sequence of entity 2 (B), FASTA

>8JXS_2 NBA3 (chains B)
QVQLQESGGGLVQAGGSLRLSCAASGSIFALNIMGWYRQAPGKQRELVAAIHSGGTTNYA
NSVKGRFTISRDNAANTVYLQMNSLKPEDTAVYYCNVKDFGAIVADRDYWGQGTQVTVSS
LEHHH

Sequence of entity 3 (C), FASTA

>8JXS_3 Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G (chains C)
MGSSHHHHHHSSGLVPRGSHMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEH
PDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRY
NGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWP
LIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNK
GETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEF
LENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAF
WYAVRTAVINAASGRQTVDQALAFAQILIMPNLTEEQRNGFIQSLKDDPSVSKEILAEAK
KLNEHQAPKGGSGGAGSGDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAK
KLNESQAGGGSGGGSGGSAVTTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVD
GVWTYDDATKTFTVTEGSG

Sequence of entity 4 (H), FASTA

>8JXS_4 Fab 8D3 heavy chain (chains H)
MDWTWRVFCLLAVAPGAHSDVQLVESGGGLVQPGKSLRLSCAASGFTFSNFGMHWVRQAP
EMGLEWVAYISSGSTTKYYGDTVKGRFTISRDNPKNTLYLQMNSLRSEDTAMYYCARRPL
YDGDYGYPMDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT
VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV
EPKSCGSHHHHHH

Sequence of entity 5 (L), FASTA

>8JXS_5 Fab 8D3 light chain (chains L)
MVLQTQVFISLLLWISGAYGNIMLTQSPSSLAVSAGERVTMSCKSTQSILYNSNQKTYLA
WYQQKPGQSPKLLIYWASTRASGVPDRFTGSGSGTDFTLTINSVQPEDLAVYYCHQYLSA
WTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQ
SGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
V6X	4-[3-methyl-4-(6-methylimidazo[1,2-a]pyrazin-5-yl)phenoxy]furo[3,2-c]pyridine	C21 H16 N4 O2	1

Primary citation

Structural basis of psychedelic LSD recognition at dopamine D 1 receptor. Fan, L., Zhuang, Y., Wu, H. et al. Neuron (2024) 112:3295. DOI 10.1016/j.neuron.2024.07.003 · 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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