8IRT: Dopamine Receptor D3R-Gi-Rotigotine complex

Dopamine Receptor D3R-Gi-Rotigotine complex. Determined by electron microscopy at 2.7 Å resolution. Released 7 Jun 2023.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Homo sapiens, Mus musculus, Escherichia coli
Chains: 5
Atoms: 8,768
Mol. weight: 173.79 kDa
Ligands: R5F
Released: 7 Jun 2023

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

Secondary structure: helices and β-sheets

8IRT contains 42 α-helices and 61 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-40	8	1
α-helix	46-54	9
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-225	6	1
α-helix	227-231	5
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
β-strand	263-268	6	1
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	330-350	21

Chain B: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-34	5
α-helix	38-39	2
β-strand	43	1	3
β-strand	47-51	5	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	78-83	6	5
β-strand	89-94	6	5
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	120-125	6	6
β-strand	134-140	7	6
β-strand	146-151	6	7
β-strand	156-161	6	7
β-strand	166-170	5	7
β-strand	175-180	6	7
α-helix	186	1
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	208-212	5	8
β-strand	217-222	6	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	259-264	6	9
β-strand	273-278	6	3
β-strand	284-289	6	3
β-strand	294-298	5	3
β-strand	304-308	5	3
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain E: 7 helices, 24 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	33-39	7	11
β-strand	45-51	7	11
α-helix	53-55	3
β-strand	58-60	3	11
β-strand	68-73	6	10
α-helix	74-76	3
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	111	1	11
β-strand	115-119	5	11
β-strand	140-141	2	12
β-strand	146-148	3	13
β-strand	155-161	7	12
β-strand	166	1	14
β-strand	172	1	14
β-strand	174-179	6	13
β-strand	186-190	5	13
β-strand	194-195	2	13
α-helix	196	1
β-strand	203-207	5	12
β-strand	211-216	6	12
α-helix	221-223	3
β-strand	225-231	7	13
α-helix	237	1
β-strand	238-239	2	13
β-strand	243-246	4	13

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	27-29	3
α-helix	30-44	15
α-helix	45-47	3
α-helix	53-55	3

Chain R: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	32-56	25
α-helix	58-60	3
α-helix	63-77	15
α-helix	78-82	5
α-helix	83-91	9
α-helix	100-133	34
α-helix	135-138	4
α-helix	144-165	22
α-helix	166-169	4
α-helix	186-193	8
α-helix	194-198	5
α-helix	199-222	24
α-helix	322-353	32
α-helix	362-380	19
α-helix	381-385	5
α-helix	388-399	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	345	Homo sapiens	P62873 (AlphaFold model)
ScFv16	E	protein	248	Mus musculus
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Soluble cytochrome b562,D(3) dopamine receptor	R	protein	545	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), P35462

Sequence of entity 1 (A), FASTA

>8IRT_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>8IRT_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (E), FASTA

>8IRT_3 ScFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Sequence of entity 4 (G), FASTA

>8IRT_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (R), FASTA

>8IRT_5 Soluble cytochrome b562,D(3) dopamine receptor (chains R)
DYKDDDDAKLQTMHHHHHHHHHHHHHHHADLEDNWETLNDNLKVIEKADNAAQVKDALTK
MRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAE
QLKTTRNAYIQKYLASENLYFQGGTMASLSQLSSHLNYTCGAENSTGASQARPHAYYALS
YCALILAIVFGNGLVCMAVLKERALQTTTNYLVVSLAVADLLVATLVMPWVVYLEVTGGV
WNFSRICCDVFVTLDVMMCTASILNLCAISIDRYTAVVMPVHYQHGTGQSSCRRVALMIT
AVWVLAFAVSCPLLFGFNTTGDPTVCSISNPDFVIYSSVVSFYLPFGVTVLVYARIYVVL
KQRRRKRILTRQNSQCNSVRPGFPQQTLSPDPAHLELKRYYSICQDTALGGPGFQERGGE
LKREEKTRNSLSPTIAPKLSLEVRKLSNGRLSTSLKLGPLQPRGVPLREKKATQMVAIVL
GAFIVCWLPFFLTHVLNTHCQTCHVSPELYSATTWLGYVNSALNPVIYTTFNIEFRKAFL
KILSC

Ligands and cofactors

ID	Name	Formula	Copies
R5F	Rotigotine	C19 H25 N O S	1

Primary citation

Structural genomics of the human dopamine receptor system. Xu, P., Huang, S., Krumm, B.E. et al. Cell Res (2023) 33:604-616. DOI 10.1038/s41422-023-00808-0 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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