6Y1Z: Mouse serotonin 5HT3 receptor

Mouse serotonin 5HT3 receptor in complex with palonosetron. Determined by electron microscopy at 2.82 Å resolution. Released 4 Mar 2020.

Method: Electron microscopy
Resolution: 2.82 Å
Organism: Mus musculus
Chains: 5
Atoms: 16,610
Mol. weight: 327.86 kDa
Ligands: TRP, HIS, NAG, O7B
Released: 4 Mar 2020

Explore 6Y1Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y1Z contains 60 α-helices and 55 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.

Chains A, B, C, D and E: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-20	8
β-strand	37-52	16	1
β-strand	57-69	13	1
α-helix	77-80	4
β-strand	85-89	5	1
α-helix	90-92	3
β-strand	98-100	3	2
β-strand	103	1	1
β-strand	114-118	5	1
β-strand	122-134	13	1
β-strand	146-155	10	2
β-strand	163-167	5	1
α-helix	171-175	5
β-strand	187-202	16	2
β-strand	205-218	14	2
α-helix	220-222	3
α-helix	224-241	18
α-helix	246-248	3
α-helix	251-269	19
α-helix	283-308	26
α-helix	314-318	5
α-helix	319-328	10
α-helix	398-457	60

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5-hydroxytryptamine receptor 3A	A, B, C, D, E	protein	566	Mus musculus	P23979 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>6Y1Z_1 5-hydroxytryptamine receptor 3A (chains A, B, C, D, E)
MRLCIPQVLLALFLSMLTGPGEGSRRRWSHPQFEKGGGSGGGSGGGSWSHPQFEKGGGSG
GGSGGGSWSHPQFEKGGGSGGGSGGGSWSHPQFEKENLYFQGSGATQARDTTQPALLRLS
DHLLANYKKGVRPVRDWRKPTTVSIDVIMYAILNVDEKNQVLTTYIWYRQYWTDEFLQWT
PEDFDNVTKLSIPTDSIWVPDILINEFVDVGKSPNIPYVYVHHRGEVQNYKPLQLVTACS
LDIYNFPFDVQNCSLTFTSWLHTIQDINITLWRSPEEVRSDKSIFINQGEWELLEVFPQF
KEFSIDISNSYAEMKFYVIIRRRPLFYAVSLLLPSIFLMVVDIVGFCLPPDSGERVSFKI
TLLLGYSVFLIIVSDTLPATAIGTPLIGVYFVVCMALLVISLAETIFIVRLVHKQDLQRP
VPDWLRHLVLDRIAWILCLGEQPMAHRPPATFQANKTDDCSGSDLLPAMGNHCSHVGGPQ
DLEKTPRGRGSPLPPPREASLAVRGLLQELSSIRHFLEKRDEMREVARDWLRVGYVLDRL
LFRIYLLAVLAYSITLVTLWSIWHSS

Ligands and cofactors

ID	Name	Formula	Copies
TRP	Tryptophan	C11 H12 N2 O2	5
HIS	Histidine	C6 H10 N3 O2	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
O7B	(3~{a}~{S})-2-[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]-3~{a},4,5,6-tetrahydro-3~…	C19 H24 N2 O	5

Primary citation

The Binding of Palonosetron and Other Antiemetic Drugs to the Serotonin 5-HT3 Receptor. Zarkadas, E., Zhang, H., Cai, W. et al. Structure (2020) 28:1131-1140.e4. DOI 10.1016/j.str.2020.07.004 · PubMed

Other PDB entries of the same protein (UniProt P23979 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8FRX 2.7 Å, Full-length mouse 5-HT3A receptor in complex with SMP100, pre-activated
8FRZ 2.75 Å, Full-length mouse 5-HT3A receptor in complex with serotonin, pre-activated
8FSB 2.75 Å, Full-length mouse 5-HT3A receptor in complex with serotonin, open-like
6Y5A 2.8 Å, Serotonin-bound 5-HT3A receptor in Salipro
6NP0 2.92 Å, Cryo-EM structure of 5HT3A receptor in presence of granisetron
6W1J 2.92 Å, Cryo-EM structure of 5HT3A receptor in presence of Alosetron
8FRW 2.92 Å, Full-length mouse 5-HT3A receptor in complex with ALB148471, pre-activated
8CC7 3.0 Å, Mouse serotonin 5-HT3A receptor in complex with PZ-1939
8AW2 3.01 Å, Mouse serotonin 5-HT3A receptor in complex with vortioxetine
6W1M 3.06 Å, Cryo-EM structure of 5HT3A receptor in presence of Ondansetron
6Y5B 3.1 Å, 5-HT3A receptor in Salipro (apo, asymmetric)
6HIQ 3.2 Å, Mouse serotonin 5-HT3 receptor, serotonin-bound, I2 conformation

Browse structure collections

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