6W1M: 5HT3A receptor in presence of Ondansetron

Cryo-EM structure of 5HT3A receptor in presence of Ondansetron. Determined by electron microscopy at 3.06 Å resolution. Released 13 Jan 2021.

Method: Electron microscopy
Resolution: 3.06 Å
Organism: Mus musculus
Chains: 5
Atoms: 16,885
Mol. weight: 268.85 kDa
Ligands: S87
Released: 13 Jan 2021

Explore 6W1M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W1M 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	14-19	6
α-helix	36	1
β-strand	37-52	16	1
β-strand	57-69	13	1
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	220-224	5
α-helix	229-239	11
α-helix	250-270	21
α-helix	282-307	26
α-helix	315-317	3
α-helix	319-322	4
α-helix	398-414	17
α-helix	416-460	45

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

>6W1M_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
S87	ondansetron	C18 H19 N3 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
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

About this viewer

MolViewer shows 6W1M directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.