6Y5B: 5-HT3A receptor in Salipro

5-HT3A receptor in Salipro (apo, asymmetric). Determined by electron microscopy at 3.1 Å resolution. Released 23 Dec 2020.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Mus musculus
Chains: 5
Atoms: 15,635
Mol. weight: 303.34 kDa
Released: 23 Dec 2020

Explore 6Y5B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y5B contains 58 α-helices and 78 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: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	39-42	4	1
β-strand	45-52	8	2
β-strand	57-64	8	2
β-strand	65-74	10	1
β-strand	85-89	5	1
α-helix	90-92	3
β-strand	98-99	2	3
β-strand	103	1	2
β-strand	114-118	5	1
β-strand	120-124	5	1
β-strand	127-134	8	2
β-strand	146-149	4	4
β-strand	153	1	4
β-strand	154-155	2	3
β-strand	165-167	3	1
α-helix	171-176	6
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	249-272	24
α-helix	282-309	28
α-helix	319-332	14
α-helix	405-421	17
α-helix	426-433	8
α-helix	435-460	26

Chain B: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	39-52	14	5
β-strand	57-74	18	5
β-strand	87-89	3	5
α-helix	90-92	3
β-strand	98-99	2	6
β-strand	103-105	3	5
β-strand	114-117	4	5
β-strand	120-124	5	5
β-strand	127-134	8	5
β-strand	146-147	2	7
β-strand	150	1	7
β-strand	153	1	7
β-strand	154-155	2	6
β-strand	165-167	3	5
α-helix	171-175	5
β-strand	187-200	14	7
β-strand	206-218	13	7
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-243	15
α-helix	245	1
α-helix	249-272	24
β-strand	276	1	8
β-strand	279	1	8
α-helix	282-308	27
α-helix	318-327	10
α-helix	404-413	10
α-helix	415-459	45

Chain C: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	39-52	14	9
β-strand	57-74	18	9
α-helix	77-80	4
β-strand	85-89	5	9
α-helix	90-92	3
β-strand	98-99	2	10
β-strand	103	1	9
β-strand	114-118	5	9
β-strand	120-134	15	9
α-helix	142-144	3
β-strand	146-148	3	11
β-strand	152-153	2	12
β-strand	154-155	2	10
β-strand	165-167	3	9
α-helix	171-175	5
β-strand	187-193	7	11
β-strand	196-200	5	12
β-strand	206-211	6	12
β-strand	213-218	6	11
α-helix	221-243	23
α-helix	250-272	23
α-helix	282-308	27
α-helix	318-331	14
α-helix	405-415	11
α-helix	420-461	42

Chain D: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	39-42	4	13
β-strand	45-52	8	14
β-strand	57-64	8	14
β-strand	65-69	5	13
β-strand	85-89	5	13
α-helix	90-92	3
β-strand	98-99	2	15
β-strand	103	1	14
β-strand	114-118	5	13
β-strand	122-124	3	13
β-strand	127-134	8	14
β-strand	146-147	2	16
β-strand	154-155	2	15
β-strand	165-167	3	13
α-helix	171-175	5
β-strand	187-202	16	16
β-strand	205-218	14	16
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-242	14
α-helix	250-272	23
α-helix	283-307	25
α-helix	320-329	10
α-helix	404-418	15
α-helix	420-461	42

Chain E: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
β-strand	39-42	4	17
β-strand	45-52	8	18
β-strand	57-64	8	18
β-strand	65-69	5	17
α-helix	77-80	4
β-strand	85-89	5	17
α-helix	90-92	3
β-strand	98-99	2	19
β-strand	103	1	18
β-strand	114-118	5	17
β-strand	122-124	3	17
β-strand	127-134	8	18
β-strand	148-149	2	19
β-strand	153-155	3	19
β-strand	165-167	3	17
α-helix	171-176	6
β-strand	187-199	13	19
β-strand	207-218	12	19
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-242	14
α-helix	249-272	24
α-helix	282-308	27
α-helix	318-331	14
α-helix	405-417	13
α-helix	423-461	39

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

>6Y5B_1 5-hydroxytryptamine receptor 3A (chains A, B, C, D, E)
MWSHPQFEKGGGSGGGSGGGSWSHPQFEKGGGSGGGSGGGSWSHPQFEKGGGSGGGSGGG
SWSHPQFEKENLYFQGATQARDTTQPALLRLSDHLLANYKKGVRPVRDWRKPTTVSIDVI
MYAILNVDEKNQVLTTYIWYRQYWTDEFLQWTPEDFDNVTKLSIPTDSIWVPDILINEFV
DVGKSPNIPYVYVHHRGEVQNYKPLQLVTACSLDIYNFPFDVQNCSLTFTSWLHTIQDIN
ITLWRSPEEVRSDKSIFINQGEWELLEVFPQFKEFSIDISNSYAEMKFYVIIRRRPLFYA
VSLLLPSIFLMVVDIVGFCLPPDSGERVSFKITLLLGYSVFLIIVSDTLPATAIGTPLIG
VYFVVCMALLVISLAETIFIVRLVHKQDLQRPVPDWLRHLVLDRIAWILCLGEQPMAHRP
PATFQANKTDDCSGSDLLPAMGNHCSHVGGPQDLEKTPRGRGSPLPPPREASLAVRGLLQ
ELSSIRHFLEKRDEMREVARDWLRVGYVLDRLLFRIYLLAVLAYSITLVTLWSIWHSS

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
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
6HIQ 3.2 Å, Mouse serotonin 5-HT3 receptor, serotonin-bound, I2 conformation

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