6Y5A: Serotonin-bound 5-HT3A receptor in Salipro

Serotonin-bound 5-HT3A receptor in Salipro. Determined by electron microscopy at 2.8 Å resolution. Released 23 Dec 2020.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Mus musculus
Chains: 5
Atoms: 16,131
Mol. weight: 304.22 kDa
Ligands: SRO
Released: 23 Dec 2020

Explore 6Y5A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y5A contains 63 α-helices and 59 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: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	39-50	12	1
β-strand	57-69	13	1
α-helix	77-80	4
β-strand	85-88	4	1
α-helix	90-92	3
β-strand	98-100	3	2
β-strand	103	1	1
β-strand	115-118	4	1
β-strand	122-134	13	1
β-strand	146-155	10	2
β-strand	165-167	3	1
α-helix	171-175	5
β-strand	187-199	13	2
β-strand	207-218	12	2
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-243	15
α-helix	249-272	24
α-helix	283-308	26
α-helix	319-332	14
α-helix	403-414	12
α-helix	415-417	3
α-helix	421-461	41

Chain B: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	37-52	16	7
β-strand	57-69	13	7
β-strand	85-88	4	7
α-helix	90-92	3
β-strand	98-100	3	8
β-strand	103	1	7
β-strand	115-118	4	7
β-strand	122-134	13	7
β-strand	146-149	4	8
β-strand	153-155	3	8
β-strand	163-167	5	7
α-helix	171-175	5
β-strand	187-199	13	8
β-strand	207-218	12	8
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-243	15
α-helix	248-272	25
α-helix	283-304	22
α-helix	305-310	6
α-helix	322-332	11
α-helix	402-417	16
α-helix	424-461	38

Chain C: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	36	1
β-strand	37-50	14	3
β-strand	57-69	13	3
β-strand	85-88	4	3
α-helix	90-92	3
β-strand	98-100	3	4
β-strand	115-118	4	3
β-strand	122-134	13	3
β-strand	146-150	5	4
β-strand	153-155	3	4
β-strand	163-167	5	3
α-helix	171-175	5
β-strand	187-199	13	4
β-strand	207-218	12	4
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-243	15
α-helix	246	1
α-helix	251-270	20
α-helix	283-307	25
α-helix	322-332	11
α-helix	404-416	13
α-helix	423-461	39

Chain D: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	39-50	12	5
β-strand	57-69	13	5
β-strand	85-89	5	5
α-helix	90-92	3
β-strand	98-100	3	6
β-strand	105	1	5
β-strand	114-118	5	5
β-strand	122-134	13	5
β-strand	146-150	5	6
β-strand	153-155	3	6
β-strand	165-167	3	5
α-helix	171-175	5
β-strand	187-200	14	6
β-strand	206-218	13	6
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-243	15
α-helix	251-272	22
α-helix	283-310	28
α-helix	319-332	14
α-helix	400-403	4
α-helix	405-417	13
α-helix	423-461	39

Chain E: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	39-52	14	9
β-strand	57-67	11	9
β-strand	69	1	10
α-helix	77-80	4
β-strand	85-89	5	11
β-strand	98-100	3	12
α-helix	110-111	2
β-strand	114-118	5	11
β-strand	122	1	10
β-strand	123-124	2	11
β-strand	125-134	10	9
β-strand	146-155	10	12
β-strand	165-167	3	9
α-helix	171-176	6
β-strand	187-200	14	12
β-strand	206-218	13	12
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-240	12
α-helix	249-272	24
α-helix	282-304	23
α-helix	305-309	5
α-helix	320-331	12
α-helix	402-415	14
α-helix	422-461	40

Molecules and chains

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

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

>6Y5A_1 5-hydroxytryptamine receptor 3A (chains A, B, C, D, E)
MWSHPQFEKGGGSGGGSGGGSWSHPQFEKGGGSGGGSGGGSWSHPQFEKGGGSGGGSGGG
SWSHPQFEKENLYFQGATQARDTTQPALLRLSDHLLANYKKGVRPVRDWRKPTTVSIDVI
MYAILNVDEKNQVLTTYIWYRQYWTDEFLQWTPEDFDNVTKLSIPTDSIWVPDILINEFV
DVGKSPNIPYVYVHHRGEVQNYKPLQLVTACSLDIYNFPFDVQNCSLTFTSWLHTIQDIN
ITLWRSPEEVRSDKSIFINQGEWELLEVFPQFKEFSIDISNSYAEMKFYVIIRRRPLFYA
VSLLLPSIFLMVVDIVGFCLPPDSGERVSFKITLLLGYSVFLIIVSDTLPATAIGTPLIG
VYFVVCMALLVISLAETIFIVRLVHKQDLQRPVPDWLRHLVLDRIAWILCLGEQPMAHRP
PATFQANKTDDCSGSDLLPAMGNHCSHVGGPQDLEKTPRGRGSPLPPPREASLAVRGLLQ
ELSSIRHFLEKRDEMREVARDWLRVGYVLDRLLFRIYLLAVLAYSITLVTLWSIWHSS

Ligands and cofactors

ID	Name	Formula	Copies
SRO	Serotonin	C10 H12 N2 O	5

Primary citation

Asymmetric opening of the homopentameric 5-HT 3A serotonin receptor in lipid bilayers. Zhang, Y., Dijkman, P.M., Zou, R. et al. Nat Commun (2021) 12:1074-1074. DOI 10.1038/s41467-021-21016-7 · 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
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)
6HIQ 3.2 Å, Mouse serotonin 5-HT3 receptor, serotonin-bound, I2 conformation

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