4PIR: Mouse serotonin 5-HT3 receptor

X-ray structure of the mouse serotonin 5-HT3 receptor. Determined by X-ray diffraction at 3.5 Å resolution. Released 6 Aug 2014.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Mus musculus, Lama glama
Chains: 10
Atoms: 20,739
Mol. weight: 338 kDa
Ligands: NAG
Released: 6 Aug 2014

Explore 4PIR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PIR contains 65 α-helices and 120 β-strands across 10 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.

Chains A and B: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	36	1
β-strand	37-52	16	1
β-strand	57-69	13	1
β-strand	85-89	5	1
α-helix	90-92	3
β-strand	98-100	3	2
β-strand	103	1	1
α-helix	110-112	3
β-strand	114-118	5	1
β-strand	122-134	13	1
β-strand	146-155	10	2
β-strand	163-167	5	1
α-helix	171-176	6
β-strand	187-199	13	2
β-strand	203	1	3
β-strand	207-218	12	2
α-helix	222-242	21
α-helix	250-268	19
α-helix	285-307	23
α-helix	318-321	4
α-helix	322-328	7
α-helix	329-333	5
α-helix	403-457	55

Chain C: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	36	1
β-strand	37-52	16	7
β-strand	57-69	13	7
β-strand	85-89	5	7
α-helix	90-92	3
β-strand	98-100	3	8
β-strand	103	1	7
α-helix	110-112	3
β-strand	114-118	5	7
β-strand	122-134	13	7
β-strand	146-155	10	8
β-strand	163-167	5	7
α-helix	171-176	6
β-strand	187-200	14	8
β-strand	203	1	9
β-strand	206-218	13	8
α-helix	222-242	21
α-helix	250-268	19
α-helix	285-307	23
α-helix	318-321	4
α-helix	322-328	7
α-helix	329-333	5
α-helix	403-458	56

Chain D: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	36	1
β-strand	37-52	16	10
β-strand	57-69	13	10
β-strand	85-89	5	10
α-helix	90-92	3
β-strand	98-100	3	11
β-strand	103	1	10
α-helix	110-112	3
β-strand	114-118	5	10
β-strand	122-134	13	10
β-strand	146-155	10	11
β-strand	163-167	5	10
α-helix	171-176	6
β-strand	187-199	13	11
β-strand	203	1	12
β-strand	207-218	12	11
α-helix	222-242	21
α-helix	250-268	19
α-helix	285-307	23
α-helix	318-321	4
α-helix	322-328	7
α-helix	329-333	5
α-helix	403-458	56

Chain E: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	36	1
β-strand	37-52	16	13
β-strand	57-69	13	13
β-strand	85-89	5	13
α-helix	90-92	3
β-strand	98-100	3	14
β-strand	103	1	13
α-helix	110-112	3
β-strand	114-118	5	13
β-strand	122-134	13	13
β-strand	146-155	10	14
β-strand	163-167	5	13
α-helix	171-176	6
β-strand	187-202	16	14
β-strand	203	1	15
β-strand	205-218	14	14
α-helix	222-242	21
α-helix	250-268	19
α-helix	285-307	23
α-helix	318-321	4
α-helix	322-328	7
α-helix	329-333	5
α-helix	403-457	55

Chain F: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	11	1	17
β-strand	18-25	8	16
β-strand	29-39	11	3
β-strand	45-53	9	3
β-strand	60-64	5	3
β-strand	72-77	6	16
β-strand	82-87	6	16
α-helix	92-94	3
β-strand	96-106	11	3
β-strand	110-114	5	3
β-strand	118-120	3	3
β-strand	121	1	17

Chains G, I and J: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	11-12	2	19
β-strand	18-25	8	18
β-strand	29-39	11	6
β-strand	45-53	9	6
β-strand	60-64	5	6
β-strand	72-77	6	18
β-strand	82-87	6	18
α-helix	92-94	3
β-strand	96-106	11	6
β-strand	110-114	5	6
β-strand	118-120	3	6
β-strand	121-122	2	19

Chain H: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	20
β-strand	11-12	2	21
β-strand	18-25	8	20
β-strand	30-39	10	9
β-strand	45-53	9	9
β-strand	60-64	5	9
β-strand	72-77	6	20
β-strand	82-87	6	20
α-helix	92-94	3
β-strand	96-105	10	9
β-strand	110-114	5	9
β-strand	118-120	3	9
β-strand	121-122	2	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5-hydroxytryptamine receptor 3A	A, B, C, D, E	protein	456	Mus musculus	P23979 (AlphaFold model)
VHH15	F, G, H, I, J	protein	124	Lama glama

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

>4PIR_1 5-hydroxytryptamine receptor 3A (chains A, B, C, D, E)
ATQARDTTQPALLRLSDHLLANYKKGVRPVRDWRKPTTVSIDVIMYAILNVDEKNQVLTT
YIWYRQYWTDEFLQWTPEDFDNVTKLSIPTDSIWVPDILINEFVDVGKSPNIPYVYVHHR
GEVQNYKPLQLVTACSLDIYNFPFDVQNCSLTFTSWLHTIQDINITLWRSPEEVRSDKSI
FINQGEWELLEVFPQFKEFSIDISNSYAEMKFYVIIRRRPLFYAVSLLLPSIFLMVVDIV
GFCLPPDSGERVSFKITLLLGYSVFLIIVSDTLPATAIGTPLIGVYFVVCMALLVISLAE
TIFIVRLVHKQDLQRPVPDWLRHLVLDRIAWILCLGEQPMAHRPPATFQANKTDDCSAMG
NHCSHVGGPQDLEKTPRGRGSPLPPPREASLAVRGLLQELSSIRHFLEKRDEMREVARDW
LRVGYVLDRLLFRIYLLAVLAYSITLVTLWSIWHSS

Sequence of entity 2 (F, G, H, I, J), FASTA

>4PIR_2 VHH15 (chains F, G, H, I, J)
DVQLVESGGGLVQPGGSLRLSCAYSGSLFSILRMDWYRQAPGKERELVAGITRDAAGYAD
STNYADSVKGRFTISRDSAKNTVYLQMNSLKPEDTAVYYCNADARTITGRADYWGQGTQV
TVSS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Water and common crystallization additives (SO4, CL) are not listed.

Primary citation

X-ray structure of the mouse serotonin 5-HT3 receptor. Hassaine, G., Deluz, C., Grasso, L. et al. Nature (2014) 512:276-281. DOI 10.1038/nature13552 · 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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