5AFJ: Alpha7-AChBP

alpha7-AChBP in complex with lobeline and fragment 1. Determined by X-ray diffraction at 2.2 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: HOMO SAPIENS, LYMNAEA STAGNALIS
Chains: 5
Atoms: 9,623
Mol. weight: 125.99 kDa
Ligands: NAG, MAN, BMA, L0B
Released: 6 May 2015

Explore 5AFJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5AFJ contains 20 α-helices and 71 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: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
β-strand	22	1	1
β-strand	25	1	1
α-helix	26	1
β-strand	27-42	16	2
β-strand	47-59	13	2
α-helix	61-63	3
β-strand	75-79	5	2
α-helix	80-82	3
β-strand	88-90	3	3
β-strand	93	1	2
β-strand	98-99	2	2
β-strand	104-108	5	2
β-strand	112-115	4	2
β-strand	118-124	7	2
β-strand	136-144	9	3
β-strand	152-156	5	2
β-strand	160	1	2
β-strand	170-183	14	3
β-strand	190-202	13	3

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
α-helix	25-26	2
β-strand	27-42	16	4
β-strand	47-64	18	4
β-strand	75-79	5	4
α-helix	80-82	3
β-strand	88-90	3	5
β-strand	93	1	4
β-strand	98-99	2	4
β-strand	104-108	5	4
β-strand	110-115	6	4
β-strand	118-124	7	4
β-strand	136-144	9	5
β-strand	152-156	5	4
β-strand	170-182	13	5
β-strand	191-202	12	5

Chain C: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	1-13	13
α-helix	26	1
β-strand	27-42	16	6
β-strand	47-59	13	6
α-helix	61-63	3
β-strand	75-79	5	6
α-helix	80-82	3
β-strand	88-90	3	7
β-strand	93	1	6
β-strand	98-99	2	6
β-strand	104-108	5	6
β-strand	112-115	4	6
β-strand	118-124	7	6
β-strand	136-144	9	7
β-strand	152-156	5	6
β-strand	160	1	6
β-strand	170-182	13	7
β-strand	191-202	12	7

Chain D: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	1-12	12
α-helix	26	1
β-strand	27-42	16	8
β-strand	47-64	18	8
β-strand	75-79	5	8
α-helix	80-82	3
β-strand	88-90	3	9
β-strand	93	1	8
β-strand	98-99	2	8
β-strand	104-108	5	8
β-strand	110-115	6	8
β-strand	118-124	7	8
α-helix	128-131	4
β-strand	136-144	9	9
β-strand	152-156	5	8
α-helix	157-159	3
β-strand	170-182	13	9
β-strand	191-202	12	9

Chain E: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	1-12	12
β-strand	22	1	10
β-strand	25	1	10
α-helix	26	1
β-strand	27-42	16	11
β-strand	47-64	18	11
α-helix	67-69	3
β-strand	75-79	5	11
α-helix	80-82	3
β-strand	88-90	3	12
β-strand	93	1	11
β-strand	98-99	2	11
β-strand	104-108	5	11
β-strand	110-115	6	11
β-strand	118-124	7	11
β-strand	136-144	9	12
β-strand	152-156	5	11
β-strand	170-182	13	12
β-strand	191-202	12	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7	A, B, C, D, E	protein	205	HOMO SAPIENS, LYMNAEA STAGNALIS	P36544 (AlphaFold model), P58154 (AlphaFold model)

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

>5AFJ_1 ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7 (chains A, B, C, D, E)
GEFQRKLYKELVKNYNPDVIPTQRDRPVTVYFSLSLLQIMDVDEKNQVVDVVFWLQMSWT
DHYLQWNVSEYPGVKQVSVPISSLWVPDLAAYNAISKPEVLTPQLALVNSSGHVQYLPSI
RQRFSCDVSGVDTESGATCKLKFGSWTHHSRELDLQMQEADISGYIPYSRFELVGVTQKR
SERFYECCKEPYPDVTFTVTFRKKG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10
MAN	alpha-D-mannopyranose	C6 H12 O6	1
BMA	beta-D-mannopyranose	C6 H12 O6	1
L0B	Alpha-Lobeline	C22 H27 N O2	5
42R	(3S)-6-(4-bromophenyl)-3-hydroxy-1,3-dimethyl-2,3-dihydropyridin-4(1H)-one	C13 H14 Br N O2	10

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

Primary citation

Molecular Blueprint of Allosteric Binding Sites in a Homologue of the Agonist-Binding Domain of the Alpha7 Nicotinic Acetylcholine Receptor. Spurny, R., Debaveye, S., Farinha, A. et al. Proc Natl Acad Sci U S A (2015) 112:E2543. DOI 10.1073/PNAS.1418289112 · PubMed

Other PDB entries of the same protein (UniProt P36544 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8P1H 1.95 Å, Crystal structure of the chimera of human 14-3-3 zeta and phosphorylated cytoplasmic…
5AFN 2.15 Å, alpha7-AChBP in complex with lobeline and fragment 5
9QTO 2.16 Å, Human alpha7 nicotinic receptor in complex with the E6 nanobody
8V8A 2.19 Å, Alpha7-nicotinic acetylcholine receptor time resolved bound to epibatidine and…
9QTN 2.28 Å, Human alpha7 nicotinic receptor in complex with the F1 nanobody
8C9X 2.3 Å, human alpha7 nicotinic receptor in complex with the C4 nanobody
8UT1 2.3 Å, Alpha7-nicotinic acetylcholine receptor bound to epibatidine
8UTB 2.3 Å, Alpha7-nicotinic acetylcholine receptor bound to epibatidine and NS-1738
8UZJ 2.3 Å, Alpha7-nicotinic acetylcholine receptor bound to epibatidine and ivermectin
8V88 2.3 Å, Alpha7-nicotinic acetylcholine receptor bound to epibatidine and GAT107
8V80 2.34 Å, Alpha7-nicotinic acetylcholine receptor bound to epibatidine and (-)-TQS
5AFK 2.38 Å, alpha7-AChBP in complex with lobeline and fragment 2

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