PDB-7ndv: X-ray structure of acetylcholine-binding protein (AChBP) in compl...

ID or keywords:

Entry

Database: PDB / ID: 7ndv

Title

X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001888.

Components

Acetylcholine-binding protein

Keywords

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

Function / homology

Function and homology information

acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity /

synaptic cleft / response to nicotine / neuron projection /

synapse /

membrane
Similarity search - Function

Biological species

Lymnaea stagnalis (great pond snail)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 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: RSC Advances / Year: 2021
Title: Discovery of fragments inducing conformational effects in dynamic proteins using a second-harmonic generation biosensor
Authors: Fitzgerald, E.A. / Butko, M.T. / Boronat, P. / Cederfelt, D. / Abramsson, M. / Ludviksdottir, H. / van Muijlwijk-Koezen, J. / de Esch, I.J.P. / Dobritzsch, D. / Young, T. / Danielson, U.H.

History

Deposition	Feb 2, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 7, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ndv.cif.gz	441 KB	Display	PDBx/mmCIF format
PDB format	pdb7ndv.ent.gz	361 KB	Display	PDB format
PDBx/mmJSON format	7ndv.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/nd/7ndv ftp://data.pdbj.org/pub/pdb/validation_reports/nd/7ndv	HTTPS FTP

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Related structure data

Related structure data	1uw6S S: Starting model for refinement
Similar structure data	3wip-1 3u8l-1 3u8n-1 3wtk-d 7ndp-2 4alx-2 1uw6-2 3u8k-4 4um3-8 3zdh-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

274 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&software
Evidence: gel filtration, The assembly was supported with Second harmonic generation experiments.
137 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&software
Evidence: gel filtration, The assembly was supported with Second harmonic generation experiments.
137 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.680, 121.270, 239.300
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	GLY	GLY	A	A	20 - 224	20 - 224
2	2	GLY	GLY	C	C	20 - 224	20 - 224
1	3	GLY	GLY	A	A	20 - 224	20 - 224
2	3	GLY	GLY	D	D	20 - 224	20 - 224
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	GLY	GLY	A	A	20 - 224	20 - 224
2	8	GLY	GLY	I	I	20 - 224	20 - 224
1	9	LYS	LYS	A	A	20 - 222	20 - 222
2	9	LYS	LYS	J	J	20 - 222	20 - 222
1	10	LYS	LYS	B	B	20 - 223	20 - 223
2	10	LYS	LYS	C	C	20 - 223	20 - 223
1	11	LYS	LYS	B	B	20 - 223	20 - 223
2	11	LYS	LYS	D	D	20 - 223	20 - 223
1	12	LYS	LYS	B	B	20 - 222	20 - 222
2	12	LYS	LYS	E	E	20 - 222	20 - 222
1	13	LYS	LYS	B	B	20 - 222	20 - 222
2	13	LYS	LYS	F	F	20 - 222	20 - 222
1	14	ILE	ILE	B	B	20 - 228	20 - 228
2	14	ILE	ILE	G	G	20 - 228	20 - 228
1	15	ILE	ILE	B	B	20 - 228	20 - 228
2	15	ILE	ILE	H	H	20 - 228	20 - 228
1	16	LYS	LYS	B	B	20 - 223	20 - 223
2	16	LYS	LYS	I	I	20 - 223	20 - 223
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 - 222	20 - 222
2	19	LYS	LYS	E	E	20 - 222	20 - 222
1	20	LYS	LYS	C	C	20 - 223	20 - 223
2	20	LYS	LYS	F	F	20 - 223	20 - 223
1	21	LYS	LYS	C	C	20 - 223	20 - 223
2	21	LYS	LYS	G	G	20 - 223	20 - 223
1	22	LYS	LYS	C	C	20 - 223	20 - 223
2	22	LYS	LYS	H	H	20 - 223	20 - 223
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 - 223	20 - 223
2	24	LYS	LYS	J	J	20 - 223	20 - 223
1	25	LYS	LYS	D	D	20 - 223	20 - 223
2	25	LYS	LYS	E	E	20 - 223	20 - 223
1	26	LYS	LYS	D	D	20 - 223	20 - 223
2	26	LYS	LYS	F	F	20 - 223	20 - 223
1	27	LYS	LYS	D	D	20 - 223	20 - 223
2	27	LYS	LYS	G	G	20 - 223	20 - 223
1	28	LYS	LYS	D	D	20 - 223	20 - 223
2	28	LYS	LYS	H	H	20 - 223	20 - 223
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 - 223	20 - 223
2	31	LYS	LYS	F	F	20 - 223	20 - 223
1	32	LYS	LYS	E	E	20 - 222	20 - 222
2	32	LYS	LYS	G	G	20 - 222	20 - 222
1	33	LYS	LYS	E	E	20 - 222	20 - 222
2	33	LYS	LYS	H	H	20 - 222	20 - 222
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 - 222	20 - 222
2	36	LYS	LYS	G	G	20 - 222	20 - 222
1	37	LYS	LYS	F	F	20 - 222	20 - 222
2	37	LYS	LYS	H	H	20 - 222	20 - 222
1	38	LYS	LYS	F	F	20 - 223	20 - 223
2	38	LYS	LYS	I	I	20 - 223	20 - 223
1	39	LYS	LYS	F	F	20 - 223	20 - 223
2	39	LYS	LYS	J	J	20 - 223	20 - 223
1	40	ILE	ILE	G	G	20 - 228	20 - 228
2	40	ILE	ILE	H	H	20 - 228	20 - 228
1	41	LYS	LYS	G	G	20 - 223	20 - 223
2	41	LYS	LYS	I	I	20 - 223	20 - 223
1	42	LYS	LYS	G	G	20 - 222	20 - 222
2	42	LYS	LYS	J	J	20 - 222	20 - 222
1	43	LYS	LYS	H	H	20 - 223	20 - 223
2	43	LYS	LYS	I	I	20 - 223	20 - 223
1	44	LYS	LYS	H	H	20 - 222	20 - 222
2	44	LYS	LYS	J	J	20 - 222	20 - 222
1	45	LYS	LYS	I	I	20 - 223	20 - 223
2	45	LYS	LYS	J	J	20 - 223	20 - 223

NCS ensembles :

#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: Chemical

ChemComp-U8Q / 4-[4-(trifluoromethyl)phenoxy]piperidine

Mass: 245.241 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₁₂H₁₄F₃NO / Feature type: SUBJECT OF INVESTIGATION

#3: 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.: 5 / Source method: obtained synthetically / 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

#4: Chemical

ChemComp-SO4 / SULFATE ION /

Sulfate

Mass: 96.063 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: SO₄

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 1115 / Source method: isolated from a natural source / Formula: H₂O

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: 2.06 Å³/Da / Density % sol: 40.17 %
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: 1.7→50 Å / Num. obs: 244709 / % possible obs: 100 % / Redundancy: 13.67 % / CC_1/2: 0.999 / Net I/σ(I): 14.05
Reflection shell	Resolution: 1.7→1.7 Å / Num. unique obs: 38136 / CC_1/2: 0.413

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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
Starting model: 1UW6

1uw6

Resolution: 1.7→48.27 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.955 / SU B: 3.664 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23314	12236	5 %	RANDOM
R_work	0.20503	-	-	-
obs	0.20644	232473	99.97 %	-

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: 39.309 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.03 Å²	0 Å²	-0 Å²
2-	-	-1.12 Å²	0 Å²
3-	-	-	-0.91 Å²

Refinement step

Cycle: 1 / Resolution: 1.7→48.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16304	0	243	1118	17665

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	17085
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	15355
X-RAY DIFFRACTION	r_angle_refined_deg	1.612	1.651	23367
X-RAY DIFFRACTION	r_angle_other_deg	1.349	1.579	35716
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.441	5	2074
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.1	21.903	951
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.937	15	2805
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.155	15	140
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	2325
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	18929
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3625
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	3.489	3.842	8197
X-RAY DIFFRACTION	r_mcbond_other	3.483	3.841	8196
X-RAY DIFFRACTION	r_mcangle_it	4.784	5.736	10229
X-RAY DIFFRACTION	r_mcangle_other	4.784	5.737	10230
X-RAY DIFFRACTION	r_scbond_it	4.799	4.483	8888
X-RAY DIFFRACTION	r_scbond_other	4.79	4.478	8873
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.183	6.48	13090
X-RAY DIFFRACTION	r_long_range_B_refined	9.146	45.386	18420
X-RAY DIFFRACTION	r_long_range_B_other	9.138	45.077	18164
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	6287	0.09
1	2	B	6287	0.09
2	1	A	6307	0.1
2	2	C	6307	0.1
3	1	A	6293	0.1
3	2	D	6293	0.1
4	1	A	6232	0.1
4	2	E	6232	0.1
5	1	A	6285	0.09
5	2	F	6285	0.09
6	1	A	6283	0.1
6	2	G	6283	0.1
7	1	A	6248	0.1
7	2	H	6248	0.1
8	1	A	6330	0.09
8	2	I	6330	0.09
9	1	A	6194	0.1
9	2	J	6194	0.1
10	1	B	6198	0.09
10	2	C	6198	0.09
11	1	B	6213	0.09
11	2	D	6213	0.09
12	1	B	6171	0.08
12	2	E	6171	0.08
13	1	B	6122	0.1
13	2	F	6122	0.1
14	1	B	6242	0.1
14	2	G	6242	0.1
15	1	B	6257	0.11
15	2	H	6257	0.11
16	1	B	6213	0.09
16	2	I	6213	0.09
17	1	B	6160	0.09
17	2	J	6160	0.09
18	1	C	6192	0.1
18	2	D	6192	0.1
19	1	C	6103	0.09
19	2	E	6103	0.09
20	1	C	6186	0.1
20	2	F	6186	0.1
21	1	C	6281	0.08
21	2	G	6281	0.08
22	1	C	6232	0.09
22	2	H	6232	0.09
23	1	C	6227	0.09
23	2	I	6227	0.09
24	1	C	6171	0.1
24	2	J	6171	0.1
25	1	D	6345	0.08
25	2	E	6345	0.08
26	1	D	6197	0.11
26	2	F	6197	0.11
27	1	D	6264	0.1
27	2	G	6264	0.1
28	1	D	6240	0.1
28	2	H	6240	0.1
29	1	D	6461	0.07
29	2	I	6461	0.07
30	1	D	6351	0.07
30	2	J	6351	0.07
31	1	E	6130	0.1
31	2	F	6130	0.1
32	1	E	6108	0.09
32	2	G	6108	0.09
33	1	E	6142	0.09
33	2	H	6142	0.09
34	1	E	6324	0.08
34	2	I	6324	0.08
35	1	E	6356	0.07
35	2	J	6356	0.07
36	1	F	6257	0.11
36	2	G	6257	0.11
37	1	F	6235	0.11
37	2	H	6235	0.11
38	1	F	6213	0.1
38	2	I	6213	0.1
39	1	F	6128	0.11
39	2	J	6128	0.11
40	1	G	6436	0.11
40	2	H	6436	0.11
41	1	G	6307	0.1
41	2	I	6307	0.1
42	1	G	6201	0.1
42	2	J	6201	0.1
43	1	H	6306	0.09
43	2	I	6306	0.09
44	1	H	6148	0.1
44	2	J	6148	0.1
45	1	I	6361	0.08
45	2	J	6361	0.08

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.376	896	-
R_work	0.393	17027	-
obs	-	-	99.87 %

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi