8CC6: Mouse serotonin 5-HT3A receptor

Mouse serotonin 5-HT3A receptor in complex with PZ-1922. Determined by electron microscopy at 3.2 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Mus musculus
Chains: 5
Atoms: 16,640
Mol. weight: 325.65 kDa
Ligands: U9L, NAG
Released: 11 Oct 2023

Explore 8CC6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CC6 contains 74 α-helices and 65 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.

Chain A: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	37-52	16	1
β-strand	57-69	13	1
α-helix	77-79	3
β-strand	85-89	5	1
α-helix	90-92	3
β-strand	98-100	3	2
β-strand	103-105	3	1
β-strand	114-118	5	1
β-strand	122-134	13	1
α-helix	142-144	3
β-strand	146-155	10	2
β-strand	163-167	5	1
α-helix	171-175	5
β-strand	187-200	14	2
β-strand	206-218	13	2
α-helix	220-222	3
α-helix	224-242	19
α-helix	246-248	3
α-helix	251-269	19
β-strand	276	1	3
β-strand	279	1	3
α-helix	283-308	26
α-helix	314-318	5
α-helix	319-323	5
α-helix	324-329	6
α-helix	330-332	3
α-helix	398-459	62

Chain B: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	37-52	16	4
β-strand	57-69	13	4
α-helix	77-80	4
β-strand	85-89	5	4
α-helix	90-92	3
β-strand	98-100	3	5
β-strand	103-105	3	4
β-strand	114-118	5	4
β-strand	122-134	13	4
α-helix	142-144	3
β-strand	146-155	10	5
β-strand	163-167	5	4
α-helix	171-175	5
β-strand	187-200	14	5
β-strand	206-218	13	5
α-helix	220-222	3
α-helix	224-242	19
α-helix	246-248	3
α-helix	251-269	19
β-strand	276	1	6
β-strand	279	1	6
α-helix	283-308	26
α-helix	314-318	5
α-helix	319-323	5
α-helix	324-329	6
α-helix	330-332	3
α-helix	398-459	62

Chain C: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	36	1
β-strand	37-52	16	7
β-strand	57-74	18	7
α-helix	77-79	3
β-strand	85-89	5	7
α-helix	90-92	3
β-strand	98-100	3	8
β-strand	103-106	4	7
β-strand	114-118	5	7
β-strand	120-134	15	7
α-helix	142-144	3
β-strand	146-155	10	8
β-strand	163-167	5	7
α-helix	171-175	5
β-strand	187-200	14	8
β-strand	206-218	13	8
α-helix	221-242	22
α-helix	246-248	3
α-helix	251-269	19
β-strand	276	1	9
β-strand	279	1	9
α-helix	283-308	26
α-helix	316-318	3
α-helix	319-323	5
α-helix	324-329	6
α-helix	330-332	3
α-helix	398-459	62

Chain D: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	37-52	16	10
β-strand	57-69	13	10
α-helix	77-80	4
β-strand	85-89	5	10
α-helix	90-92	3
β-strand	98-100	3	11
β-strand	103-105	3	10
β-strand	114-118	5	10
β-strand	122-134	13	10
α-helix	142-144	3
β-strand	146-155	10	11
β-strand	163-167	5	10
α-helix	171-175	5
β-strand	187-200	14	11
β-strand	206-218	13	11
α-helix	221-242	22
α-helix	246-248	3
α-helix	251-269	19
β-strand	276	1	12
β-strand	279	1	12
α-helix	283-308	26
α-helix	314-318	5
α-helix	319-323	5
α-helix	324-329	6
α-helix	330-332	3
α-helix	398-459	62

Chain E: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	37-52	16	13
β-strand	57-69	13	13
α-helix	77-79	3
β-strand	85-89	5	13
α-helix	90-92	3
β-strand	98-100	3	14
β-strand	103-105	3	13
β-strand	114-118	5	13
β-strand	122-134	13	13
α-helix	142-144	3
β-strand	146-155	10	14
β-strand	163-167	5	13
α-helix	171-175	5
β-strand	187-200	14	14
β-strand	206-218	13	14
α-helix	220-222	3
α-helix	224-242	19
α-helix	246-248	3
α-helix	251-269	19
β-strand	276	1	15
β-strand	279	1	15
α-helix	283-308	26
α-helix	316-318	3
α-helix	319-323	5
α-helix	324-329	6
α-helix	330-332	3
α-helix	398-459	62

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

>8CC6_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
U9L	1-[(3-chlorophenyl)methyl]-4-piperazin-1-yl-pyrrolo[3,2-c]quinoline	C22 H21 Cl N4	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Superiority of the Triple-Acting 5-HT 6 R/5-HT 3 R Antagonist and MAO-B Reversible Inhibitor PZ-1922 over 5-HT 6 R Antagonist Intepirdine in Alleviation of Cognitive Deficits in Rats. Grychowska, K., Lopez-Sanchez, U., Vitalis, M. et al. J Med Chem (2023) 66:14928-14947. DOI 10.1021/acs.jmedchem.3c01482 · 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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