7VGY: Melatonin receptor1-2-Iodomelatonin-Gicomplex

Melatonin receptor1-2-Iodomelatonin-Gicomplex. Determined by electron microscopy at 3.1 Å resolution. Released 2 Mar 2022.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, Rattus norvegicus, Bos taurus
Chains: 5
Atoms: 8,748
Mol. weight: 152.94 kDa
Ligands: CLR, ML2
Released: 2 Mar 2022

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

Secondary structure: helices and β-sheets

7VGY contains 36 α-helices and 62 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: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	24-54	31
α-helix	64-78	15
α-helix	80-88	9
α-helix	97-129	33
α-helix	135-138	4
α-helix	141-158	18
α-helix	162-165	4
β-strand	168-171	4	1
β-strand	176-179	4	1
α-helix	185-195	11
α-helix	197-204	8
α-helix	208-221	14
α-helix	236-237	2
α-helix	238-242	5
α-helix	247-250	4
α-helix	252-258	7
α-helix	265-268	4
α-helix	269-271	3
α-helix	274-296	23
α-helix	300-312	13

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-30	25
β-strand	33-38	6	2
α-helix	45-53	9
β-strand	185-190	6	2
β-strand	195-200	6	2
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-223	4	2
β-strand	226	1	3
α-helix	242-254	13
β-strand	263-267	5	2
β-strand	269	1	3
α-helix	271-277	7
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-322	4	2
α-helix	330-351	22

Chain C: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	30-33	4
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	88-94	7	5
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	121-125	5	6
β-strand	134-137	4	6
β-strand	146-151	6	7
β-strand	156-161	6	7
β-strand	165-170	6	7
β-strand	175-181	7	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	208-212	5	8
β-strand	218-222	5	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	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	304-307	4	10
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	10-21	12
α-helix	30-43	14
α-helix	45-47	3
α-helix	56-58	3

Chain E: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	18-25	8	11
β-strand	33-39	7	12
β-strand	45-51	7	12
α-helix	53-55	3
β-strand	58-60	3	12
β-strand	65	1	11
β-strand	68-73	6	11
β-strand	78-83	6	11
β-strand	92-94	3	13
β-strand	95-99	5	12
β-strand	110-111	2	12
β-strand	115-117	3	13
β-strand	141-142	2	14
β-strand	146-148	3	15
β-strand	155-160	6	14
β-strand	166	1	16
β-strand	172	1	16
β-strand	174-179	6	15
β-strand	186-190	5	15
β-strand	194-195	2	15
α-helix	196	1
β-strand	203-208	6	14
β-strand	211-216	6	14
β-strand	225-231	7	15
α-helix	237	1
β-strand	243-246	4	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Melatonin receptor type 1A	A	protein	350	Homo sapiens	P48039 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	protein	353	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	345	Rattus norvegicus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	67	Bos taurus	P63212 (AlphaFold model)
scFv16	E	protein	256	Mus musculus

Sequence of entity 1 (A), FASTA

>7VGY_1 Melatonin receptor type 1A (chains A)
MQGNGSALPNASQPVLRGDGARPSWLASALACVLIFTIVVDILGNLLVILSVYRNKKLRN
AGNIFVVSLAVADLVVAIYPYPLVLMSIFNNGWNLGYLHCQVSGFLMGLSVIGSIFNITG
IAINRYCYICHSLKYDKLYSSKNSLCYVLLIWLLTLAAVLPNLRAGTLQYDPRIYSCTFA
QSVSSAYTIAVVVFHFLVPMIIVIFCYLRIWILVLQVRQRVKPDRKPKLKPQDFRNFVTM
FVVFVLFAICWAPLNFIGLAVASDPASMVPRIPEWLFVASYYMAYFNSCLNAIIYGLLNQ
NFRKEYRRIIVSLCTARVFFVDSSNDVADRVKWKPSPLMTNNNVVKVDSV

Sequence of entity 2 (B), FASTA

>7VGY_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
GCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGY
SEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKT
TGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAA
YIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (C), FASTA

>7VGY_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
GPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (D), FASTA

>7VGY_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Sequence of entity 5 (E), FASTA

>7VGY_5 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1
ML2	N-[2-(2-iodo-5-methoxy-1H-indol-3-yl)ethyl]acetamide	C13 H15 I N2 O2	1

Primary citation

Structural basis of the ligand binding and signaling mechanism of melatonin receptors. Wang, Q., Lu, Q., Guo, Q. et al. Nat Commun (2022) 13:454-454. DOI 10.1038/s41467-022-28111-3 · PubMed

Other PDB entries of the same protein (UniProt P48039 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ME2 2.8 Å, XFEL crystal structure of human melatonin receptor MT1 in complex with ramelteon
6ME3 2.9 Å, XFEL crystal structure of human melatonin receptor MT1 in complex with 2-phenylmelatonin
6ME4 3.2 Å, XFEL crystal structure of human melatonin receptor MT1 in complex with 2-iodomelatonin
6ME5 3.2 Å, XFEL crystal structure of human melatonin receptor MT1 in complex with agomelatine
6PS8 3.3 Å, XFEL MT1R structure by ligand exchange from agomelatine to 2-phenylmelatonin.
7DB6 3.3 Å, human melatonin receptor MT1 - Gi1 complex
7VGZ 3.3 Å, MT1-remalteon-Gi complex

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