7DB6: Human melatonin receptor MT1 - Gi1 complex

human melatonin receptor MT1 - Gi1 complex. Determined by electron microscopy at 3.3 Å resolution. Released 18 Aug 2021.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Rattus rattus, Bos taurus
Chains: 5
Atoms: 8,767
Mol. weight: 155.96 kDa
Ligands: JEV
Released: 18 Aug 2021

Explore 7DB6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DB6 contains 30 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 A: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	9-31	23
β-strand	34-40	7	1
β-strand	186-191	6	1
β-strand	194-199	6	1
α-helix	213-215	3
β-strand	220-224	5	1
α-helix	228-230	3
α-helix	243-253	11
β-strand	264-265	2	2
β-strand	266-267	2	1
β-strand	268	1	3
α-helix	278-280	3
α-helix	297-309	13
β-strand	319-320	2	2
β-strand	323	1	3
α-helix	329-331	3
α-helix	337-351	15

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	7-24	18
α-helix	30-34	5
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	120-125	6	6
β-strand	134-140	7	6
β-strand	146-153	8	7
β-strand	156-161	6	7
β-strand	165-168	4	7
β-strand	178-181	4	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	207-212	6	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	260-263	4	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	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	13-21	9
α-helix	34-43	10
α-helix	54-55	2

Chain D: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	25-50	26
α-helix	61-78	18
α-helix	81-90	10
α-helix	97-129	33
α-helix	135-138	4
α-helix	143-159	17
β-strand	169-170	2	16
β-strand	177-178	2	16
α-helix	185-192	8
α-helix	198-216	19
α-helix	234-241	8
α-helix	245-260	16
α-helix	265-271	7
α-helix	274-297	24
α-helix	300-303	4

Chain E: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	33-40	8	12
β-strand	44-51	8	12
α-helix	53-55	3
β-strand	58-60	3	12
β-strand	68-73	6	11
β-strand	78-83	6	11
β-strand	92-99	8	12
β-strand	111	1	12
β-strand	115-119	5	12
α-helix	125-127	3
β-strand	128-130	3	13
β-strand	135-136	2	14
β-strand	143-149	7	13
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	14
β-strand	174-177	4	14
β-strand	183	1	14
β-strand	191-196	6	13
β-strand	199-204	6	13
β-strand	213-219	7	14
α-helix	225	1
β-strand	227	1	14
β-strand	231-234	4	14

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	344	Rattus rattus	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	68	Bos taurus	P63212 (AlphaFold model)
scFv16	E	protein	260	Mus musculus
Melatonin receptor type 1A	D	protein	372	Homo sapiens	P48039 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7DB6_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>7DB6_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GSQLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>7DB6_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFS

Sequence of entity 4 (E), FASTA

>7DB6_4 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAASSEDLYFQ

Sequence of entity 5 (D), FASTA

>7DB6_5 Melatonin receptor type 1A (chains D)
MKTIIALSYIFCLVFADYKDDDDKEFMQGNGSALPNASQPVLRGDGARPSWLASALACVL
IFTIVVDILGNLLVILSVYRNKKLRNAGNIFVVSLAVADLVVAIYPYPLVLMSIFNNGWN
LGYLHCQVSGFLMGLSVIGSIFNITGIAINRYCYICHSLKYDKLYSSKNSLCYVLLIWLL
TLAAVLPNLRAGTLQYDPRIYSCTFAQSVSSAYTIAVVVFHFLVPMIIVIFCYLRIWILV
LQVRQRVKPDRKPKLKPQDFRNFVTMFVVFVLFAICWAPLNFIGLAVASDPASMVPRIPE
WLFVASYYMAYFNSCLNAIIYGLLNQNFRKEYRRIIVSLCTARVFFVDSSNDVADRVKWK
PSPLMTENLYFQ

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

Primary citation

Cryo-EM structure of the human MT 1 -G i signaling complex. Okamoto, H.H., Miyauchi, H., Inoue, A. et al. Nat Struct Mol Biol (2021) 28:694-701. DOI 10.1038/s41594-021-00634-1 · 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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