6VMS: PDB entry 6VMS

Structure of a D2 dopamine receptor-G-protein complex in a lipid membrane. Determined by electron microscopy at 3.8 Å resolution. Released 17 Jun 2020.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Rattus norvegicus, Homo sapiens, Enterobacteria phage T4
Chains: 5
Atoms: 8,953
Mol. weight: 166.76 kDa
Ligands: 08Y
Released: 17 Jun 2020

Explore 6VMS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VMS contains 38 α-helices and 58 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, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-40	8	1
α-helix	46-52	7
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-231	5
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	274-280	7
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	331-351	21

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-51	5	2
β-strand	58-63	6	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	120-125	6	4
β-strand	134-140	7	4
β-strand	146-153	8	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	176-181	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	217-223	7	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-264	6	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	293-298	6	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 C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain E: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	33-40	8	10
β-strand	44-51	8	10
β-strand	59-60	2	10
β-strand	68-73	6	9
α-helix	74-76	3
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	110-111	2	10
β-strand	115-119	5	10
β-strand	140-142	3	11
β-strand	146-148	3	12
β-strand	155-161	7	11
β-strand	166	1	13
β-strand	172	1	13
β-strand	174-179	6	12
β-strand	186-190	5	12
β-strand	194-195	2	12
α-helix	196	1
β-strand	203-208	6	11
β-strand	211-216	6	11
α-helix	221-223	3
β-strand	226-231	6	12
α-helix	237	1
β-strand	238-239	2	12
β-strand	243-246	4	12

Chain R: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	36-41	6
α-helix	42-61	20
α-helix	68-82	15
α-helix	83-87	5
α-helix	88-96	9
α-helix	106-137	32
α-helix	145-167	23
α-helix	168-170	3
α-helix	187-194	8
α-helix	195-199	5
α-helix	200-223	24
α-helix	364-398	35
α-helix	405-425	21
α-helix	431-440	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Rattus norvegicus	P10824 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	82	Homo sapiens	P59768 (AlphaFold model)
scFv16	E	protein	259	Homo sapiens
Endolysin,D(2) dopamine receptor,D(2) dopamine receptor	R	protein	450	Enterobacteria phage T4, Homo sapiens	D9IEF7, P14416

Sequence of entity 1 (A), FASTA

>6VMS_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>6VMS_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>6VMS_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MGHHHHHHHHGGASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDP
LLTPVPASENPFREKKFFCAIL

Sequence of entity 4 (E), FASTA

>6VMS_4 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Sequence of entity 5 (R), FASTA

>6VMS_5 Endolysin,D(2) dopamine receptor,D(2) dopamine receptor (chains R)
DYKDDDDANIFEMLRIDEGLRLKIYKNTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRN
TNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAG
FTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYAADRPHYNYYAT
LLTLLIAVIVFGNVLVCMAVSREKALQTTTNYLIVSLAVADLLVATLVMPWVVYLEVVGE
WKFSRIHCDIFVTLDVMMCTASILNLCAISIDRYTAVAMPMLYNTRYSSKRRVTVMISIV
WVLSFTISCPLLFGLNNADQNECIIANPAFVVYSSIVSFYVPFIVILLVYIKIYIVLRRR
RKLVNTNRKLSQQKEKKATQLLAIYLGLFIICWLPFFITHILNIHCDCNIPPVLYSAFTW
LGYVNSAINPIIYTTFNIEFRKAFLKILHC

Ligands and cofactors

ID	Name	Formula	Copies
08Y	bromoergocryptine	C32 H40 Br N5 O5	1

Primary citation

Structure of a D2 dopamine receptor-G-protein complex in a lipid membrane. Yin, J., Chen, K.M., Clark, M.J. et al. Nature (2020) 584:125-129. DOI 10.1038/s41586-020-2379-5 · PubMed

Other PDB entries of the same protein (UniProt P10824 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1CIP 1.5 Å, Gi-alpha-1 subunit of guanine nucleotide-binding protein complexed with a GTP analogue
1SVS 1.5 Å, Structure of the K180P mutant of Gi alpha subunit bound to GppNHp.
4N0D 1.55 Å, Crystal structure of the K345L variant of the Gi alpha1 subunit bound to GTPgammaS
5KDO 1.9 Å, Heterotrimeric complex of the 4 alanine insertion variant of the Gi alpha1 subunit and…
1AS0 2.0 Å, GTP-gamma-S bound G42V GIA1
1GIA 2.0 Å, Structure of active conformations of GIA1 and the mechanism of GTP hydrolysis
1SVK 2.0 Å, Structure of the K180P mutant of Gi alpha subunit bound to AlF4 and GDP
4PAQ 2.0 Å, A conserved phenylalanine as relay between the 5 helix and the GDP binding region of…
4PAO 2.0 Å, A conserved phenylalanine as relay between the 5 helix and the GDP binding region of…
1FQJ 2.02 Å, Crystal structure of the heterotrimeric complex of the rgs domain of RGS9, the gamma…
6M8H 2.07 Å, Crystal Structure of the R208Q mutant of G(i) subunit alpha-1
1BH2 2.1 Å, A326S mutant of an inhibitory alpha subunit

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