6W1Y: 5HT3A receptor in presence of Palonosetron

Cryo-EM structure of 5HT3A receptor in presence of Palonosetron. Determined by electron microscopy at 3.35 Å resolution. Released 13 Jan 2021.

Method: Electron microscopy
Resolution: 3.35 Å
Organism: Mus musculus
Chains: 5
Atoms: 16,845
Mol. weight: 268.87 kDa
Ligands: O7B
Released: 13 Jan 2021

Explore 6W1Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W1Y contains 55 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: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-19	7
α-helix	36	1
β-strand	37-52	16	1
β-strand	57-68	12	1
β-strand	87-89	3	1
α-helix	90-92	3
β-strand	98-100	3	2
β-strand	103	1	1
β-strand	114-117	4	1
β-strand	123-133	11	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	220-223	4
α-helix	229-241	13
α-helix	250-270	21
α-helix	285-307	23
α-helix	313-317	5
α-helix	328-331	4
α-helix	398-460	63

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5-hydroxytryptamine receptor 3A	A, B, C, D, E	protein	450	Mus musculus	P23979 (AlphaFold model)

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

>6W1Y_1 5-hydroxytryptamine receptor 3A (chains A, B, C, D, E)
TTQPALLRLSDHLLANYKKGVRPVRDWRKPTTVSIDVIMYAILNVDEKNQVLTTYIWYRQ
YWTDEFLQWTPEDFDNVTKLSIPTDSIWVPDILINEFVDVGKSPNIPYVYVHHRGEVQNY
KPLQLVTACSLDIYNFPFDVQNCSLTFTSWLHTIQDINITLWRSPEEVRSDKSIFINQGE
WELLEVFPQFKEFSIDISNSYAEMKFYVIIRRRPLFYAVSLLLPSIFLMVVDIVGFCLPP
DSGERVSFKITLLLGYSVFLIIVSDTLPATAIGTPLIGVYFVVCMALLVISLAETIFIVR
LVHKQDLQRPVPDWLRHLVLDRIAWILCLGEQPMAHRPPATFQANKTDDCSAMGNHCSHV
GGPQDLEKTPRGRGSPLPPPREASLAVRGLLQELSSIRHFLEKRDEMREVARDWLRVGYV
LDRLLFRIYLLAVLAYSITLVTLWSIWHYS

Ligands and cofactors

ID	Name	Formula	Copies
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

High-resolution structures of multiple 5-HT 3A R-setron complexes reveal a novel mechanism of competitive inhibition. Basak, S., Kumar, A., Ramsey, S. et al. Elife (2020) 9. DOI 10.7554/eLife.57870 · 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
6Y1Z 2.82 Å, Mouse serotonin 5HT3 receptor in complex with palonosetron
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)

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