6ME4: PDB entry 6ME4

XFEL crystal structure of human melatonin receptor MT1 in complex with 2-iodomelatonin. Determined by X-ray diffraction at 3.2 Å resolution. Released 24 Apr 2019.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, Pyrococcus abyssi GE5
Chains: 1
Atoms: 3,736
Mol. weight: 57.15 kDa
Ligands: ML2
Released: 24 Apr 2019

Explore 6ME4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ME4 contains 29 α-helices and 10 β-strands across 1 chain. 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: 29 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	24-54	31
α-helix	61-63	3
α-helix	64-78	15
α-helix	80-90	11
α-helix	97-134	38
α-helix	138-139	2
α-helix	144-159	16
α-helix	161-165	5
β-strand	168-171	4	1
β-strand	176-179	4	1
α-helix	185-192	8
α-helix	193-197	5
α-helix	198-1001	22
α-helix	1009-1011	3
α-helix	1016-1027	12
β-strand	1033-1038	6	2
β-strand	1041	1	3
α-helix	1048-1058	11
α-helix	1062-1066	5
β-strand	1067-1072	6	2
β-strand	1075	1	3
α-helix	1077-1089	13
β-strand	1093-1096	4	2
α-helix	1099-1101	3
α-helix	1102-1111	10
β-strand	1114-1117	4	2
α-helix	1126-1133	8
β-strand	1137-1141	5	2
α-helix	1146-1149	4
β-strand	1156-1158	3	2
α-helix	1163-1174	12
α-helix	1178-1195	18
α-helix	1196-229	3
α-helix	235-263	29
α-helix	265-271	7
α-helix	274-286	13
α-helix	287-289	3
α-helix	290-298	9
α-helix	300-312	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase	A	protein	503	Homo sapiens, Pyrococcus abyssi GE5	P48039 (AlphaFold model), Q9V2J8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6ME4_1 chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase (chains A)
GTSQPVLRGDGARPSWLASALACVLIFTIVVDILGNLLVILSVYRNKKLRNAGNIFVVSL
AVANLVVAIYPYPLVLMSIFNNGWNFGYLHCQVSAFLMGLSVIGSIWNITGIAIDRYLYI
CHSLKYDKLYSSKNSLCYVLLIWLLTLAAVLPNLRAGTLQYDPRIYSCTFAQSVSSAYTI
AVVVFHFLVPMIIVIFCYLRIWILVLQVRGIDCSFWNESYLTGSRDERKKSLLSKFGMDE
GVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHG
NVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIIT
NETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSKLKPQDFRNFVTMFV
VFVLFAICFAPLNFIGLAVASDPASMVPRIPEWLFVASYYMAYFNSCLNPIIYGLLDQNF
RKEYRRIIVSLCTARVFFVDSSN

Ligands and cofactors

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

Water and common crystallization additives (GOL, PEG) are not listed.

Primary citation

Structural basis of ligand recognition at the human MT1melatonin receptor. Stauch, B., Johansson, L.C., McCorvy, J.D. et al. Nature (2019) 569:284-288. DOI 10.1038/s41586-019-1141-3 · 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
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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