7VGZ: MT1-remalteon-Gi complex

MT1-remalteon-Gi complex. Determined by electron microscopy at 3.3 Å resolution. Released 2 Mar 2022.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Rattus norvegicus, Bos taurus
Chains: 5
Atoms: 8,790
Mol. weight: 152.84 kDa
Ligands: JEV, CLR
Released: 2 Mar 2022

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

Secondary structure: helices and β-sheets

7VGZ contains 38 α-helices and 63 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 B: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	24-54	31
α-helix	64-74	11
α-helix	80-90	11
α-helix	97-129	33
α-helix	135-138	4
α-helix	141-159	19
α-helix	162-165	4
β-strand	168-171	4	1
β-strand	176-179	4	1
α-helix	185-192	8
α-helix	193-197	5
α-helix	198-219	22
α-helix	231-237	7
α-helix	238-242	5
α-helix	243-244	2
α-helix	247-250	4
α-helix	252-263	12
α-helix	265-271	7
α-helix	274-294	21
α-helix	300-312	13

Chain C: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	35-39	5	2
α-helix	46-54	9
β-strand	185-187	3	2
β-strand	197-200	4	2
α-helix	208-210	3
β-strand	220-226	7	2
α-helix	227-229	3
α-helix	242-254	13
β-strand	263-269	7	2
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	2
α-helix	330-351	22

Chain D: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146	1	6
β-strand	150-151	2	7
β-strand	156-160	5	7
β-strand	161	1	6
β-strand	166-170	5	7
β-strand	178-180	3	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	207-212	6	8
β-strand	220-223	4	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	273-276	4	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	303-308	6	10
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	335-339	5	3

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	30-43	14
α-helix	45-47	3

Chain F: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	17-25	9	11
β-strand	33-39	7	13
β-strand	45-51	7	13
α-helix	53-55	3
β-strand	58-60	3	13
α-helix	62-64	3
β-strand	68-73	6	11
β-strand	78-84	7	11
α-helix	88-90	3
β-strand	92-94	3	12
β-strand	95-99	5	13
β-strand	110-111	2	13
β-strand	115-119	5	12
β-strand	140-142	3	14
β-strand	146-148	3	15
β-strand	156-161	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	226-231	6	15
α-helix	237	1
β-strand	239	1	15
β-strand	243-246	4	15

Molecules and chains

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

Sequence of entity 1 (B), FASTA

>7VGZ_1 Melatonin receptor type 1A (chains B)
MQGNGSALPNASQPVLRGDGARPSWLASALACVLIFTIVVDILGNLLVILSVYRNKKLRN
AGNIFVVSLAVADLVVAIYPYPLVLMSIFNNGWNLGYLHCQVSGFLMGLSVIGSIFNITG
IAINRYCYICHSLKYDKLYSSKNSLCYVLLIWLLTLAAVLPNLRAGTLQYDPRIYSCTFA
QSVSSAYTIAVVVFHFLVPMIIVIFCYLRIWILVLQVRQRVKPDRKPKLKPQDFRNFVTM
FVVFVLFAICWAPLNFIGLAVASDPASMVPRIPEWLFVASYYMAYFNSCLNAIIYGLLNQ
NFRKEYRRIIVSLCTARVFFVDSSNDVADRVKWKPSPLMTNNNVVKVDSV

Sequence of entity 2 (C), FASTA

>7VGZ_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
GCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGY
SEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKT
TGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAA
YIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (D), FASTA

>7VGZ_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains D)
GPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (E), FASTA

>7VGZ_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains E)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Sequence of entity 5 (F), FASTA

>7VGZ_5 scFv16 (chains F)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
JEV	N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide	C16 H21 N O2	1
CLR	Cholesterol	C27 H46 O	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
7VGY 3.1 Å, Melatonin receptor1-2-Iodomelatonin-Gicomplex
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

Browse structure collections

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