6NP0: 5HT3A receptor in presence of granisetron

Cryo-EM structure of 5HT3A receptor in presence of granisetron. Determined by electron microscopy at 2.92 Å resolution. Released 24 Jul 2019.

Method: Electron microscopy
Resolution: 2.92 Å
Organism: Mus musculus
Chains: 5
Atoms: 16,891
Mol. weight: 290.28 kDa
Ligands: NAG, CWB
Released: 24 Jul 2019

Explore 6NP0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NP0 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	222-224	3
α-helix	228-241	14
α-helix	246-248	3
α-helix	250-270	21
α-helix	282-307	26
α-helix	315-317	3
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	489	Mus musculus	P23979 (AlphaFold model)

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

>6NP0_1 5-hydroxytryptamine receptor 3A (chains A, B, C, D, E)
MRLCIPQVLLALFLSMLTAPGEGSRRRATQARDTTQPALLRLSDHLLANYKKGVRPVRDW
RKPTTVSIDVIMYAILNVDEKNQVLTTYIWYRQYWTDEFLQWTPEDFDNVTKLSIPTDSI
WVPDILINEFVDVGKSPNIPYVYVHHRGEVQNYKPLQLVTACSLDIYNFPFDVQNCSLTF
TSWLHTIQDINITLWRSPEEVRSDKSIFINQGEWELLEVFPQFKEFSIDISNSYAEMKFY
VIIRRRPLFYAVSLLLPSIFLMVVDIVGFCLPPDSGERVSFKITLLLGYSVFLIIVSDTL
PATAIGTPLIGVYFVVCMALLVISLAETIFIVRLVHKQDLQRPVPDWLRHLVLDRIAWIL
CLGEQPMAHRPPATFQANKTDDCSGSDLLPAMGNHCSHVGGPQDLEKTPRGRGSPLPPPR
EASLAVRGLLQELSSIRHFLEKRDEMREVARDWLRVGYVLDRLLFRIYLLAVLAYSITLV
TLWSIWHYS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10
CWB	1-methyl-N-[(1R,5S)-9-methyl-9-azabicyclo[3.3.1]nonan-3-yl]indazole-3-carboxami…	C18 H24 N4 O	5

Water and common crystallization additives (CL) are not listed.

Primary citation

Molecular mechanism of setron-mediated inhibition of full-length 5-HT3Areceptor. Basak, S., Gicheru, Y., Kapoor, A. et al. Nat Commun (2019) 10:3225-3225. DOI 10.1038/s41467-019-11142-8 · 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
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

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