6DG7: 5-hydroxytryptamine receptor 3A

Full-length 5-HT3A receptor in a serotonin-bound conformation- State 1. Determined by electron microscopy at 3.32 Å resolution. Released 7 Nov 2018.

Method: Electron microscopy
Resolution: 3.32 Å
Organism: Mus musculus
Chains: 5
Atoms: 16,720
Mol. weight: 270.68 kDa
Ligands: SRO
Released: 7 Nov 2018

Explore 6DG7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DG7 contains 55 α-helices and 55 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.

Chains A, B, C, D and E: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-19	7
α-helix	36	1
β-strand	37-52	16	1
β-strand	57-69	13	1
β-strand	87-88	2	1
β-strand	99	1	2
β-strand	103	1	1
α-helix	106-108	3
β-strand	115-116	2	1
β-strand	122-134	13	1
β-strand	148-154	7	2
β-strand	163-166	4	1
α-helix	171-175	5
β-strand	187-200	14	2
β-strand	206-218	13	2
α-helix	219	1
α-helix	222-241	20
α-helix	250-270	21
α-helix	282-307	26
α-helix	315-317	3
α-helix	318-331	14
α-helix	398-461	64

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5-hydroxytryptamine receptor 3A	A, B, C, D, E	protein	455	Mus musculus	P23979 (AlphaFold model)

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

>6DG7_1 5-hydroxytryptamine receptor 3A (chains A, B, C, D, E)
TQPALLRLSDHLLANYKKGVRPVRDWRKPTTVSIDVIMYAILNVDEKNQVLTTYIWYRQY
WTDEFLQWTPEDFDNVTKLSIPTDSIWVPDILINEFVDVGKSPNIPYVYVHHRGEVQNYK
PLQLVTACSLDIYNFPFDVQNCSLTFTSWLHTIQDINITLWRSPEEVRSDKSIFINQGEW
ELLEVFPQFKEFSIDISNSYAEMKFYVIIRRRPLFYAVSLLLPSIFLMVVDIVGFCLPPD
SGERVSFKITLLLGYSVFLIIVSDTLPATAIGTPLIGVYFVVCMALLVISLAETIFIVRL
VHKQDLQRPVPDWLRHLVLDRIAWILCLGEQPMAHRPPATFQANKTDDCSGSDLLPAMGN
HCSHVGGPQDLEKTPRGRGSPLPPPREASLAVRGLLQELSSIRHFLEKRDEMREVARDWL
RVGYVLDRLLFRIYLLAVLAYSITLVTLWSIWHYS

Ligands and cofactors

ID	Name	Formula	Copies
SRO	Serotonin	C10 H12 N2 O	5

Primary citation

Cryo-EM reveals two distinct serotonin-bound conformations of full-length 5-HT3Areceptor. Basak, S., Gicheru, Y., Rao, S. et al. Nature (2018) 563:270-274. DOI 10.1038/s41586-018-0660-7 · 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
6Y5B 3.1 Å, 5-HT3A receptor in Salipro (apo, asymmetric)

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