8C20: Tetrameric 5-HT3aR in Salipro

Tetrameric 5-HT3aR in Salipro (holo state, symmetric). Determined by electron microscopy at 3.5 Å resolution. Released 10 Jul 2024.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Mus musculus
Chains: 4
Atoms: 11,701
Mol. weight: 243.02 kDa
Ligands: SRO
Released: 10 Jul 2024

Explore 8C20 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8C20 contains 48 α-helices and 45 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: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	37-52	16	1
β-strand	57-74	18	1
β-strand	85-89	5	1
β-strand	98-100	3	2
β-strand	103-106	4	1
β-strand	114-118	5	1
β-strand	120-129	10	1
β-strand	131-134	4	1
β-strand	146-155	10	2
β-strand	163-167	5	1
α-helix	171-175	5
β-strand	187-196	10	2
β-strand	209-218	10	2
α-helix	220-223	4
α-helix	224-228	5
α-helix	229-242	14
α-helix	249-270	22
α-helix	283-285	3
α-helix	286-290	5
α-helix	291-310	20
α-helix	316-318	3
α-helix	319-332	14
α-helix	423-458	36

Chain B: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-22	11
β-strand	37-52	16	3
β-strand	57-69	13	3
α-helix	77-80	4
β-strand	86-88	3	3
β-strand	98-100	3	4
β-strand	103-105	3	3
β-strand	115-118	4	3
β-strand	122-134	13	3
β-strand	146-147	2	4
β-strand	152-155	4	4
β-strand	163-167	5	3
α-helix	171-175	5
β-strand	187-200	14	4
β-strand	206-218	13	4
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-243	15
α-helix	250-272	23
α-helix	284-308	25
α-helix	319-332	14
α-helix	422-461	40

Chain C: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	12-22	11
β-strand	40-52	13	5
α-helix	54-56	3
β-strand	57-67	11	5
α-helix	77-80	4
β-strand	85-89	5	5
β-strand	103-105	3	5
β-strand	114-118	5	5
β-strand	123-134	12	5
β-strand	146-153	8	6
β-strand	166-167	2	5
α-helix	171-176	6
α-helix	177-180	4
β-strand	187-196	10	6
β-strand	210-218	9	6
α-helix	223	1
α-helix	224-228	5
α-helix	229-240	12
α-helix	249-272	24
α-helix	282-284	3
α-helix	286-309	24
α-helix	319-332	14
α-helix	422-461	40

Chain D: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-22	10
β-strand	37-52	16	7
β-strand	57-69	13	7
β-strand	85-89	5	7
β-strand	99-100	2	8
β-strand	105	1	7
β-strand	114-118	5	7
β-strand	122-134	13	7
α-helix	139-141	3
β-strand	146-154	9	8
β-strand	163-167	5	7
α-helix	171-176	6
β-strand	187-199	13	8
β-strand	207-218	12	8
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
α-helix	284-308	25
α-helix	321-328	8
α-helix	422	1
α-helix	423-427	5
α-helix	428-461	34

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

>8C20_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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