8C21: Tetrameric 5-HT3A receptor in Salipro

Tetrameric 5-HT3A receptor in Salipro (holo, asymmetric). Determined by electron microscopy at 3.6 Å resolution. Released 10 Jul 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Mus musculus
Chains: 4
Atoms: 11,954
Mol. weight: 243.02 kDa
Ligands: SRO
Released: 10 Jul 2024

Explore 8C21 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8C21 contains 47 α-helices and 63 β-strands across 4 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: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-21	11
β-strand	37-52	16	1
β-strand	57-68	12	1
α-helix	77-79	3
β-strand	85-89	5	1
β-strand	99-100	2	2
β-strand	103-105	3	1
β-strand	114-118	5	1
β-strand	123-129	7	1
β-strand	132-133	2	1
β-strand	146-149	4	2
β-strand	152-154	3	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	221-223	3
α-helix	224-228	5
α-helix	229-243	15
α-helix	252-272	21
α-helix	282-310	29
α-helix	322-324	3
α-helix	325-329	5
α-helix	422-461	40

Chain B: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	36	1
β-strand	37-52	16	3
β-strand	57-69	13	3
β-strand	85	1	4
β-strand	89	1	5
α-helix	90-92	3
β-strand	98-100	3	6
β-strand	103-105	3	3
α-helix	109-111	3
β-strand	114	1	5
β-strand	116-117	2	3
β-strand	118	1	4
β-strand	122-134	13	3
β-strand	146-155	10	6
β-strand	163-167	5	3
α-helix	171-175	5
β-strand	187-196	10	6
β-strand	199-200	2	7
β-strand	206-207	2	7
β-strand	210-218	9	6
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-240	12
α-helix	241-243	3
α-helix	250-272	23
β-strand	276	1	8
β-strand	279	1	8
α-helix	282-308	27
α-helix	323-332	10
α-helix	423-461	39

Chain C: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	12-19	8
α-helix	36	1
β-strand	37-47	11	9
β-strand	58-69	12	9
β-strand	85-88	4	9
α-helix	90-92	3
β-strand	98-99	2	10
β-strand	103-105	3	9
β-strand	115-118	4	9
β-strand	122-124	3	9
β-strand	127-133	7	9
β-strand	146-150	5	11
β-strand	153-155	3	10
β-strand	163-167	5	9
α-helix	171-175	5
β-strand	187-195	9	11
β-strand	199	1	12
β-strand	207	1	12
β-strand	209-210	2	10
β-strand	211-218	8	11
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-243	15
α-helix	251-272	22
α-helix	282-304	23
α-helix	307-311	5
α-helix	321-332	12
α-helix	423-460	38

Chain D: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	14-21	8
α-helix	36-37	2
β-strand	40-41	2	13
β-strand	44-52	9	14
β-strand	57-63	7	14
β-strand	66-67	2	13
β-strand	86-88	3	13
β-strand	98-100	3	15
β-strand	115-117	3	13
β-strand	123-125	3	13
β-strand	128-130	3	14
β-strand	133	1	14
β-strand	146-149	4	16
β-strand	153-155	3	15
α-helix	171-177	7
β-strand	187-196	10	16
β-strand	200	1	17
β-strand	206	1	17
β-strand	210-218	9	16
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-241	13
α-helix	250-272	23
α-helix	282-307	26
α-helix	315-317	3
α-helix	320-329	10
α-helix	424-461	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5-hydroxytryptamine receptor 3A	A, B, C, D	protein	538	Mus musculus	P23979 (AlphaFold model)

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

>8C21_1 5-hydroxytryptamine receptor 3A (chains A, B, C, D)
MWSHPQFEKGGGSGGGSGGGSWSHPQFEKGGGSGGGSGGGSWSHPQFEKGGGSGGGSGGG
SWSHPQFEKENLYFQGATQARDTTQPALLRLSDHLLANYKKGVRPVRDWRKPTTVSIDVI
MYAILNVDEKNQVLTTYIWYRQYWTDEFLQWTPEDFDNVTKLSIPTDSIWVPDILINEFV
DVGKSPNIPYVYVHHRGEVQNYKPLQLVTACSLDIYNFPFDVQNCSLTFTSWLHTIQDIN
ITLWRSPEEVRSDKSIFINQGEWELLEVFPQFKEFSIDISNSYAEMKFYVIIRRRPLFYA
VSLLLPSIFLMVVDIVGFCLPPDSGERVSFKITLLLGYSVFLIIVSDTLPATAIGTPLIG
VYFVVCMALLVISLAETIFIVRLVHKQDLQRPVPDWLRHLVLDRIAWILCLGEQPMAHRP
PATFQANKTDDCSGSDLLPAMGNHCSHVGGPQDLEKTPRGRGSPLPPPREASLAVRGLLQ
ELSSIRHFLEKRDEMREVARDWLRVGYVLDRLLFRIYLLAVLAYSITLVTLWSIWHSS

Ligands and cofactors

ID	Name	Formula	Copies
SRO	Serotonin	C10 H12 N2 O	2

Primary citation

Structure of tetrameric forms of the serotonin-gated 5-HT3 A receptor ion channel. Introini, B., Cui, W., Chu, X. et al. EMBO J (2024) 43:4451-4471. DOI 10.1038/s44318-024-00191-5 · 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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