PDB-8p1e: X-ray structure of acetylcholine-binding protein (AChBP) in compl...

ID or keywords:

Entry

Database: PDB / ID: 8p1e

Title

X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001613.

Components

Acetylcholine-binding protein

Keywords

CHOLINE-BINDING PROTEIN / Fragment based drug design / Acetylcholine-binding protein / choline-binding proteins

Function / homology

Function and homology information

extracellular ligand-gated monoatomic ion channel activity /

synaptic cleft / transmembrane signaling receptor activity /

synapse /

membrane
Similarity search - Function

Biological species

Lymnaea stagnalis (great pond snail)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Cederfelt, D. / Boronat, P. / Dobritzsch, D. / Hennig, S. / Fitzgerald, E.A. / de Esch, I.J.P. / Danielson, U.H.

Funding support

European Union, 1items

Citation

Journal: To Be Published
Title: Elucidating the regulation of ligand gated ion channels via biophysical studies of ligand-induced conformational dynamics of acetylcholine binding proteins
Authors: Fitzgerald, E.A. / Cederfelt, D. / Boronat, P. / Aarmo Lund, B. / de Esch, I.J.P. / Danielson, U.H.

History

Deposition	May 11, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8p1e.cif.gz	423.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8p1e.ent.gz	344.8 KB	Display	PDB format
PDBx/mmJSON format	8p1e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p1/8p1e ftp://data.pdbj.org/pub/pdb/validation_reports/p1/8p1e	HTTPS FTP

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Related structure data

Related structure data	8p11C 8p1fC 8p22C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#71 - Nov 2005 Acetylcholine Receptor similarity (5) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (4)

Deposited unit

A: Acetylcholine-binding protein

B: Acetylcholine-binding protein

C: Acetylcholine-binding protein

D: Acetylcholine-binding protein

E: Acetylcholine-binding protein

F: Acetylcholine-binding protein

G: Acetylcholine-binding protein

H: Acetylcholine-binding protein

I: Acetylcholine-binding protein

J: Acetylcholine-binding protein

hetero molecules

273 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Acetylcholine-binding protein

B: Acetylcholine-binding protein

C: Acetylcholine-binding protein

D: Acetylcholine-binding protein

E: Acetylcholine-binding protein

hetero molecules

defined by author
Evidence: surface plasmon resonance
136 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Acetylcholine-binding protein

G: Acetylcholine-binding protein

H: Acetylcholine-binding protein

I: Acetylcholine-binding protein

J: Acetylcholine-binding protein

hetero molecules

defined by author
136 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.100, 121.080, 241.210
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Refine code: 0

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	A	A	20 - 223	20 - 223
2	1	LYS	LYS	B	B	20 - 223	20 - 223
1	2	LYS	LYS	A	A	20 - 223	20 - 223
2	2	LYS	LYS	C	C	20 - 223	20 - 223
1	3	LYS	LYS	A	A	20 - 222	20 - 222
2	3	LYS	LYS	D	D	20 - 222	20 - 222
1	4	LYS	LYS	A	A	20 - 223	20 - 223
2	4	LYS	LYS	E	E	20 - 223	20 - 223
1	5	LYS	LYS	A	A	20 - 223	20 - 223
2	5	LYS	LYS	F	F	20 - 223	20 - 223
1	6	LYS	LYS	A	A	20 - 223	20 - 223
2	6	LYS	LYS	G	G	20 - 223	20 - 223
1	7	LYS	LYS	A	A	20 - 223	20 - 223
2	7	LYS	LYS	H	H	20 - 223	20 - 223
1	8	LYS	LYS	A	A	20 - 223	20 - 223
2	8	LYS	LYS	I	I	20 - 223	20 - 223
1	9	LYS	LYS	A	A	20 - 223	20 - 223
2	9	LYS	LYS	J	J	20 - 223	20 - 223
1	10	GLY	GLY	B	B	20 - 224	20 - 224
2	10	GLY	GLY	C	C	20 - 224	20 - 224
1	11	GLY	GLY	B	B	20 - 224	20 - 224
2	11	GLY	GLY	D	D	20 - 224	20 - 224
1	12	LYS	LYS	B	B	20 - 223	20 - 223
2	12	LYS	LYS	E	E	20 - 223	20 - 223
1	13	GLY	GLY	B	B	20 - 224	20 - 224
2	13	GLY	GLY	F	F	20 - 224	20 - 224
1	14	LYS	LYS	B	B	20 - 223	20 - 223
2	14	LYS	LYS	G	G	20 - 223	20 - 223
1	15	GLY	GLY	B	B	20 - 224	20 - 224
2	15	GLY	GLY	H	H	20 - 224	20 - 224
1	16	GLY	GLY	B	B	20 - 224	20 - 224
2	16	GLY	GLY	I	I	20 - 224	20 - 224
1	17	LYS	LYS	B	B	20 - 222	20 - 222
2	17	LYS	LYS	J	J	20 - 222	20 - 222
1	18	GLY	GLY	C	C	20 - 224	20 - 224
2	18	GLY	GLY	D	D	20 - 224	20 - 224
1	19	LYS	LYS	C	C	20 - 223	20 - 223
2	19	LYS	LYS	E	E	20 - 223	20 - 223
1	20	GLY	GLY	C	C	20 - 224	20 - 224
2	20	GLY	GLY	F	F	20 - 224	20 - 224
1	21	LYS	LYS	C	C	20 - 223	20 - 223
2	21	LYS	LYS	G	G	20 - 223	20 - 223
1	22	GLY	GLY	C	C	20 - 224	20 - 224
2	22	GLY	GLY	H	H	20 - 224	20 - 224
1	23	GLY	GLY	C	C	20 - 224	20 - 224
2	23	GLY	GLY	I	I	20 - 224	20 - 224
1	24	LYS	LYS	C	C	20 - 222	20 - 222
2	24	LYS	LYS	J	J	20 - 222	20 - 222
1	25	LYS	LYS	D	D	20 - 223	20 - 223
2	25	LYS	LYS	E	E	20 - 223	20 - 223
1	26	GLY	GLY	D	D	20 - 224	20 - 224
2	26	GLY	GLY	F	F	20 - 224	20 - 224
1	27	LYS	LYS	D	D	20 - 223	20 - 223
2	27	LYS	LYS	G	G	20 - 223	20 - 223
1	28	GLY	GLY	D	D	20 - 224	20 - 224
2	28	GLY	GLY	H	H	20 - 224	20 - 224
1	29	GLY	GLY	D	D	20 - 224	20 - 224
2	29	GLY	GLY	I	I	20 - 224	20 - 224
1	30	LYS	LYS	D	D	20 - 223	20 - 223
2	30	LYS	LYS	J	J	20 - 223	20 - 223
1	31	LYS	LYS	E	E	20 - 222	20 - 222
2	31	LYS	LYS	F	F	20 - 222	20 - 222
1	32	LYS	LYS	E	E	20 - 223	20 - 223
2	32	LYS	LYS	G	G	20 - 223	20 - 223
1	33	LYS	LYS	E	E	20 - 223	20 - 223
2	33	LYS	LYS	H	H	20 - 223	20 - 223
1	34	LYS	LYS	E	E	20 - 223	20 - 223
2	34	LYS	LYS	I	I	20 - 223	20 - 223
1	35	LYS	LYS	E	E	20 - 223	20 - 223
2	35	LYS	LYS	J	J	20 - 223	20 - 223
1	36	LYS	LYS	F	F	20 - 223	20 - 223
2	36	LYS	LYS	G	G	20 - 223	20 - 223
1	37	GLY	GLY	F	F	20 - 224	20 - 224
2	37	GLY	GLY	H	H	20 - 224	20 - 224
1	38	GLY	GLY	F	F	20 - 224	20 - 224
2	38	GLY	GLY	I	I	20 - 224	20 - 224
1	39	LYS	LYS	F	F	20 - 223	20 - 223
2	39	LYS	LYS	J	J	20 - 223	20 - 223
1	40	LYS	LYS	G	G	20 - 223	20 - 223
2	40	LYS	LYS	H	H	20 - 223	20 - 223
1	41	LYS	LYS	G	G	20 - 222	20 - 222
2	41	LYS	LYS	I	I	20 - 222	20 - 222
1	42	LYS	LYS	G	G	20 - 223	20 - 223
2	42	LYS	LYS	J	J	20 - 223	20 - 223
1	43	GLY	GLY	H	H	20 - 224	20 - 224
2	43	GLY	GLY	I	I	20 - 224	20 - 224
1	44	LYS	LYS	H	H	20 - 223	20 - 223
2	44	LYS	LYS	J	J	20 - 223	20 - 223
1	45	LYS	LYS	I	I	20 - 223	20 - 223
2	45	LYS	LYS	J	J	20 - 223	20 - 223

NCS ensembles :

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Protein / Sugars , 2 types, 13 molecules ABCDEFGHIJ

#1: Protein

Acetylcholine-binding protein / ACh-binding protein / AchBP

Mass: 27060.320 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Lymnaea stagnalis (great pond snail) / Production host:

Spodoptera frugiperda (fall armyworm) / References: UniProt: P58154

#2: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 4 types, 590 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-WD2 / 1-[4-(trifluoromethyl)pyridin-2-yl]piperazine Mass: 231.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₂F₃N₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.87 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG3350 3% Ammonium sulphate 1.8M HEPES buffer 0.1M, pH 7.75

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976238 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2020
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976238 Å / Relative weight: 1
Reflection	Resolution: 2.1→48.36 Å / Num. obs: 132342 / % possible obs: 99.96 % / Redundancy: 13.5 % / CC_1/2: 0.99 / R_rim(I) all: 0.3577 / Net I/σ(I): 9.73
Reflection shell	Resolution: 2.1→2.175 Å / Num. unique obs: 13095 / CC_1/2: 0.537

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
PHASER		phasing
XSCALE		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→48.36 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.942 / SU B: 7.069 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24108	6617	5 %	RANDOM
R_work	0.20825	-	-	-
obs	0.20991	125718	99.98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 47.389 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.88 Å²	-0 Å²	0 Å²
2-	-	-3.14 Å²	0 Å²
3-	-	-	2.26 Å²

Refinement step

Cycle: 1 / Resolution: 2.1→48.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16164	0	125	579	16868

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	16781
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	15048
X-RAY DIFFRACTION	r_angle_refined_deg	1.496	1.65	22926
X-RAY DIFFRACTION	r_angle_other_deg	1.249	1.58	34993
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.852	5	2038
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.51	21.989	945
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.409	15	2759
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.077	15	136
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	2274
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	18658
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3550
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.791	4.751	8109
X-RAY DIFFRACTION	r_mcbond_other	3.791	4.751	8110
X-RAY DIFFRACTION	r_mcangle_it	5.395	7.11	10112
X-RAY DIFFRACTION	r_mcangle_other	5.395	7.111	10113
X-RAY DIFFRACTION	r_scbond_it	5.12	5.408	8672
X-RAY DIFFRACTION	r_scbond_other	5.12	5.408	8673
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.615	7.874	12799
X-RAY DIFFRACTION	r_long_range_B_refined	9.927	54.17	17420
X-RAY DIFFRACTION	r_long_range_B_other	9.927	54.172	17421
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	6246	0.08
1	2	B	6246	0.08
2	1	A	6195	0.09
2	2	C	6195	0.09
3	1	A	6118	0.09
3	2	D	6118	0.09
4	1	A	6120	0.1
4	2	E	6120	0.1
5	1	A	6273	0.08
5	2	F	6273	0.08
6	1	A	6214	0.09
6	2	G	6214	0.09
7	1	A	6216	0.07
7	2	H	6216	0.07
8	1	A	6199	0.09
8	2	I	6199	0.09
9	1	A	6180	0.09
9	2	J	6180	0.09
10	1	B	6216	0.1
10	2	C	6216	0.1
11	1	B	6275	0.08
11	2	D	6275	0.08
12	1	B	6166	0.09
12	2	E	6166	0.09
13	1	B	6262	0.08
13	2	F	6262	0.08
14	1	B	6260	0.08
14	2	G	6260	0.08
15	1	B	6175	0.08
15	2	H	6175	0.08
16	1	B	6252	0.08
16	2	I	6252	0.08
17	1	B	6263	0.08
17	2	J	6263	0.08
18	1	C	6151	0.11
18	2	D	6151	0.11
19	1	C	6167	0.11
19	2	E	6167	0.11
20	1	C	6262	0.09
20	2	F	6262	0.09
21	1	C	6144	0.11
21	2	G	6144	0.11
22	1	C	6167	0.09
22	2	H	6167	0.09
23	1	C	6149	0.1
23	2	I	6149	0.1
24	1	C	6203	0.11
24	2	J	6203	0.11
25	1	D	6056	0.1
25	2	E	6056	0.1
26	1	D	6219	0.09
26	2	F	6219	0.09
27	1	D	6258	0.08
27	2	G	6258	0.08
28	1	D	6144	0.08
28	2	H	6144	0.08
29	1	D	6311	0.07
29	2	I	6311	0.07
30	1	D	6112	0.1
30	2	J	6112	0.1
31	1	E	6077	0.11
31	2	F	6077	0.11
32	1	E	6093	0.1
32	2	G	6093	0.1
33	1	E	6082	0.09
33	2	H	6082	0.09
34	1	E	6088	0.1
34	2	I	6088	0.1
35	1	E	6350	0.08
35	2	J	6350	0.08
36	1	F	6167	0.09
36	2	G	6167	0.09
37	1	F	6194	0.07
37	2	H	6194	0.07
38	1	F	6241	0.08
38	2	I	6241	0.08
39	1	F	6129	0.1
39	2	J	6129	0.1
40	1	G	6150	0.08
40	2	H	6150	0.08
41	1	G	6217	0.08
41	2	I	6217	0.08
42	1	G	6142	0.09
42	2	J	6142	0.09
43	1	H	6198	0.07
43	2	I	6198	0.07
44	1	H	6146	0.08
44	2	J	6146	0.08
45	1	I	6177	0.08
45	2	J	6177	0.08

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.368	483	-
R_work	0.34	9187	-
obs	-	-	99.95 %

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Protein / Sugars , 2 types, 13 molecules ABCDEFGHIJ

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Non-polymers , 4 types, 590 molecules

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Protein / Sugars , 2 types, 13 molecules ABCDEFGHIJ

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Non-polymers , 4 types, 590 molecules

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