8Q1M: Soluble acetylcholine receptor

Name: PDB 8Q1M: Aplysia californica acetylcholine-binding protein in complex with Spiroimine (+)-4 R
Published: 2024-04-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: choline-binding protein

Aplysia californica acetylcholine-binding protein in complex with Spiroimine (+)-4 R. Determined by X-ray diffraction at 2.0 Å resolution. Released 3 Apr 2024.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Aplysia californica
Chains: 5
Atoms: 9,462
Mol. weight: 125.9 kDa
Ligands: NAG, ILR
Released: 3 Apr 2024

Explore 8Q1M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q1M contains 25 α-helices and 77 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: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	-3-14	18
α-helix	18-20	3
β-strand	29-44	16	1
β-strand	49-66	18	1
α-helix	69-72	4
β-strand	77-81	5	1
α-helix	82-84	3
β-strand	90-92	3	2
β-strand	95	1	1
α-helix	98-99	2
β-strand	100-101	2	1
β-strand	106-110	5	1
β-strand	112-117	6	1
β-strand	120-126	7	1
β-strand	138-146	9	2
β-strand	154-157	4	1
β-strand	162	1	2
β-strand	164	1	1
β-strand	174-188	15	2
β-strand	191-206	16	2

Chain B: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	0-11	12
α-helix	12-16	5
α-helix	18-20	3
β-strand	24	1	3
β-strand	27	1	3
β-strand	29-44	16	4
β-strand	49-66	18	4
α-helix	69-72	4
β-strand	77-81	5	4
α-helix	82-84	3
β-strand	90-92	3	5
β-strand	95	1	4
β-strand	100-101	2	4
β-strand	106-110	5	4
β-strand	112-117	6	4
β-strand	120-126	7	4
β-strand	138-146	9	5
β-strand	154-157	4	4
β-strand	162	1	5
β-strand	164	1	4
β-strand	174-186	13	5
β-strand	195-206	12	5

Chain C: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	-7-14	22
α-helix	18-20	3
β-strand	29-44	16	6
β-strand	49-61	13	6
α-helix	63-65	3
α-helix	69-71	3
β-strand	77-81	5	6
α-helix	82-84	3
β-strand	90-92	3	7
β-strand	95	1	6
β-strand	100-101	2	6
β-strand	106-110	5	6
β-strand	114-117	4	6
β-strand	120-126	7	6
β-strand	138-146	9	7
β-strand	154-157	4	6
β-strand	162	1	7
β-strand	164	1	6
β-strand	174-186	13	7
β-strand	195-206	12	7

Chain D: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	0-14	15
β-strand	29-44	16	8
β-strand	49-66	18	8
α-helix	69-72	4
β-strand	77-81	5	8
α-helix	82-84	3
β-strand	90-92	3	9
β-strand	95	1	8
α-helix	98-99	2
β-strand	100-101	2	8
β-strand	106-110	5	8
β-strand	112-117	6	8
β-strand	120-126	7	8
β-strand	138-146	9	9
β-strand	154-157	4	8
β-strand	162	1	9
β-strand	164	1	8
β-strand	174-186	13	9
β-strand	195-206	12	9

Chain E: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	-1-11	13
α-helix	12-16	5
β-strand	29-44	16	10
β-strand	49-61	13	10
α-helix	63-65	3
α-helix	69-71	3
β-strand	77-81	5	10
α-helix	82-84	3
β-strand	90-92	3	11
β-strand	95	1	10
α-helix	98-99	2
β-strand	100-101	2	10
β-strand	106-110	5	10
β-strand	114-117	4	10
β-strand	120-126	7	10
β-strand	138-146	9	11
β-strand	154-157	4	10
β-strand	162	1	11
β-strand	164	1	10
β-strand	174-186	13	11
β-strand	195-206	12	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble acetylcholine receptor	A, B, C, D, E	protein	217	Aplysia californica	Q8WSF8 (AlphaFold model)

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

>8Q1M_1 Soluble acetylcholine receptor (chains A, B, C, D, E)
DYKDDDDKLHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVD
LVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTH
DGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYAS
SKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
ILR	Spiroimine (+)-4 R	C13 H21 N O2	5

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

Primary citation

The Cyclic Imine Core Common to the Marine Macrocyclic Toxins Is Sufficient to Dictate Nicotinic Acetylcholine Receptor Antagonism. Bourne, Y., Sulzenbacher, G., Chabaud, L. et al. Mar Drugs (2024) 22. DOI 10.3390/md22040149 · PubMed

Other PDB entries of the same protein (UniProt Q8WSF8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6T9R 1.72 Å, Aplysia californica AChBP in complex with a cytisine derivative
2WN9 1.75 Å, Crystal structure of Aplysia ACHBP in complex with 4-0H-DMXBA
2PGZ 1.76 Å, Crystal structure of Cocaine bound to an ACh-Binding Protein
2WNJ 1.8 Å, Crystal structure of aplysia achbp in complex with dmxba
8QTL 1.85 Å, Aplysia californica acetylcholine-binding protein in complex with Spiroimine (-)-4 S
2Y7Y 1.9 Å, Aplysia californica achbp in apo state
4XHE 1.9 Å, Crystal Structure of A-AChBP in complex with pinnatoxin A
4ZK4 1.9 Å, Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica…
2XYS 1.91 Å, Crystal structure of Aplysia californica AChBP in complex with strychnine
5TVC 1.93 Å, Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica…
3C84 1.94 Å, Crystal structure of a complex of AChBP from aplysia californica and the neonicotinoid…
2YMD 1.96 Å, Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with serotonin…

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