PDB-4nzb: NS9283 bound to Ls-AChBP

ID or keywords:

Entry

Database: PDB / ID: 4nzb

Title

NS9283 bound to Ls-AChBP

Components

Acetylcholine-binding protein

Keywords

ACETYLCHOLINE-BINDING PROTEIN / NS9283 / AChBP-modulator complex

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: 2.68 Å

Authors

Olsen, J.A. / Kastrup, J.S. / Gajhede, M.

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Structural and functional studies of the modulator NS9283 reveal agonist-like mechanism of action at alpha 4 beta 2 nicotinic acetylcholine receptors.
Authors: Olsen, J.A. / Ahring, P.K. / Kastrup, J.S. / Gajhede, M. / Balle, T.

History

Deposition	Dec 11, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 9, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 16, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Dec 25, 2019	Group: Database references / Derived calculations / Category: citation / struct_conn Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4nzb.cif.gz	597.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4nzb.ent.gz	498 KB	Display	PDB format
PDBx/mmJSON format	4nzb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nz/4nzb ftp://data.pdbj.org/pub/pdb/validation_reports/nz/4nzb	HTTPS FTP

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Related structure data

Related structure data	3zdgS S: Starting model for refinement
Similar structure data	3wip-2 3u8m-3 3u8m-1 3zdg-1 3u8n-3 4zr6-d 3zdg-2 7ndp-1 3wto-d 3u8m-2 Search similar-shape structures by Omokage search (details) 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

Related structure data

3zdgS

S: Starting model for refinement

Similar structure data

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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

G: Acetylcholine-binding protein

D: Acetylcholine-binding protein

E: Acetylcholine-binding protein

A: Acetylcholine-binding protein

B: Acetylcholine-binding protein

C: Acetylcholine-binding protein

F: Acetylcholine-binding protein

H: Acetylcholine-binding protein

I: Acetylcholine-binding protein

J: Acetylcholine-binding protein

K: Acetylcholine-binding protein

L: Acetylcholine-binding protein

M: Acetylcholine-binding protein

N: Acetylcholine-binding protein

O: Acetylcholine-binding protein

hetero molecules

365 kDa, 15 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

G: Acetylcholine-binding protein

F: Acetylcholine-binding protein

H: Acetylcholine-binding protein

I: Acetylcholine-binding protein

J: Acetylcholine-binding protein

hetero molecules

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

2

D: Acetylcholine-binding protein

E: Acetylcholine-binding protein

A: Acetylcholine-binding protein

B: Acetylcholine-binding protein

C: Acetylcholine-binding protein

hetero molecules

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

3

K: Acetylcholine-binding protein

L: Acetylcholine-binding protein

M: Acetylcholine-binding protein

N: Acetylcholine-binding protein

O: Acetylcholine-binding protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	231.726, 140.381, 119.545
Angle α, β, γ (deg.)	90.00, 89.98, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	I-421- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2

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Protein / Sugars , 2 types, 17 molecules GDEABCFHIJKLMNO

#1: Protein

Acetylcholine-binding protein / ACh-binding protein / AchBP

Mass: 23862.523 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Details: Great pond snail / Source: (natural)

Lymnaea stagnalis (great pond snail) / References: UniProt: P58154

#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.: 2
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 , 7 types, 386 molecules

#2: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol Mass: 238.278 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Chemical	ChemComp-NSE / 3-[3-(pyridin-3-yl)-1,2,4-oxadiazol-5-yl]benzonitrile / NS9283 Mass: 248.240 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₄H₈N₄O
#7: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1mM Tris, 0.95M (NH3)2SO4, 4% PEG 400, 0.1M NaCl, 2.5% DMSO, pH 8.0, vapor diffusion, sitting drop, temperature 293K

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Data collection

Diffraction

Mean temperature: 101 K

Diffraction source

Source:

SYNCHROTRON / Site:

MAX II

/ Beamline: I911-3 / Wavelength: 1 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 15, 2011

Radiation

Monochromator: Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.68→28.241 Å / Num. all: 105283 / Num. obs: 105283 / % possible obs: 98.1 % / Redundancy: 3.6 % / B_iso Wilson estimate: 52.68 Å² / R_sym value: 0.072 / Net I/σ(I): 11.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
2.68-2.82	2.3	0.379	2	0.379	1	87.6
2.82-3	3.7	0.294	2.6	0.294	1	100
3-3.2	3.8	0.173	4.4	0.173	1	100
3.2-3.46	3.8	0.107	7.1	0.107	1	100
3.46-3.79	3.8	0.075	9.8	0.075	1	100
3.79-4.24	3.8	0.06	10.1	0.06	1	100
4.24-4.89	3.8	0.052	13.3	0.052	1	100
4.89-5.99	3.8	0.051	13.1	0.051	1	100
5.99-8.47	3.8	0.045	14.9	0.045	1	100
8.47-28.241	3.7	0.041	14.6	0.041	1	97.3

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Processing

Software

Name	Version	Classification
SCALA	3.3.16	data scaling
PHENIX	1.8.4_1496	refinement
PDB_EXTRACT	3.11	data extraction
MxCuBE	/ marccd	data collection
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3ZDG (chains A-E)

3zdg

Resolution: 2.68→28.241 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.35 / σ(F): 0 / Phase error: 24.53 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.24	5277	5.01 %
R_work	0.2067	-	-
obs	0.2084	105263	98.16 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 50.3787 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.4447 Å²	-0 Å²	-5.5659 Å²
2-	-	9.5028 Å²	-0 Å²
3-	-	-	-6.0581 Å²

Refinement step

Cycle: LAST / Resolution: 2.68→28.241 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23740	0	428	335	24503

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	24710
X-RAY DIFFRACTION	f_angle_d	1.588	33611
X-RAY DIFFRACTION	f_dihedral_angle_d	14.641	9079
X-RAY DIFFRACTION	f_chiral_restr	0.055	3818
X-RAY DIFFRACTION	f_plane_restr	0.009	4287

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	C	1502	X-RAY DIFFRACTION	POSITIONAL	0.075
1	2	B	1502	X-RAY DIFFRACTION	POSITIONAL	0.075
1	3	F	1491	X-RAY DIFFRACTION	POSITIONAL	0.11
1	4	G	1497	X-RAY DIFFRACTION	POSITIONAL	0.11
1	5	I	1484	X-RAY DIFFRACTION	POSITIONAL	0.098
1	6	L	1497	X-RAY DIFFRACTION	POSITIONAL	0.098
1	7	M	1472	X-RAY DIFFRACTION	POSITIONAL	0.099
1	8	N	1502	X-RAY DIFFRACTION	POSITIONAL	0.127
1	9	J	1419	X-RAY DIFFRACTION	POSITIONAL	0.116
1	10	D	1411	X-RAY DIFFRACTION	POSITIONAL	0.135
1	11	O	1419	X-RAY DIFFRACTION	POSITIONAL	0.072
1	12	K	1400	X-RAY DIFFRACTION	POSITIONAL	0.078
1	13	E	1419	X-RAY DIFFRACTION	POSITIONAL	0.084
1	14	A	1419	X-RAY DIFFRACTION	POSITIONAL	0.079
1	15	H	1419	X-RAY DIFFRACTION	POSITIONAL	0.11
2	1	K	65	X-RAY DIFFRACTION	POSITIONAL	0.038
2	2	E	65	X-RAY DIFFRACTION	POSITIONAL	0.038
2	3	A	65	X-RAY DIFFRACTION	POSITIONAL	0.13
2	4	H	65	X-RAY DIFFRACTION	POSITIONAL	0.087

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.68-2.7104	0.3073	137	0.2858	2520	2657	74
2.7104-2.7423	0.3067	135	0.2685	2871	3006	85
2.7423-2.7757	0.2995	142	0.2735	3115	3257	90
2.7757-2.8108	0.3371	141	0.2715	3218	3359	96
2.8108-2.8478	0.3454	150	0.2551	3405	3555	100
2.8478-2.8867	0.2852	179	0.2386	3394	3573	100
2.8867-2.9279	0.2834	185	0.2558	3378	3563	100
2.9279-2.9716	0.2972	172	0.2521	3401	3573	100
2.9716-3.018	0.2869	173	0.2406	3403	3576	100
3.018-3.0674	0.2647	181	0.2323	3388	3569	100
3.0674-3.1202	0.2954	191	0.227	3367	3558	100
3.1202-3.1769	0.2938	191	0.2251	3337	3528	100
3.1769-3.2379	0.2809	185	0.2329	3412	3597	100
3.2379-3.3039	0.2918	195	0.2337	3354	3549	100
3.3039-3.3756	0.2727	165	0.225	3347	3512	100
3.3756-3.454	0.2371	186	0.2098	3397	3583	100
3.454-3.5402	0.2493	195	0.2092	3406	3601	100
3.5402-3.6358	0.2482	190	0.2073	3340	3530	100
3.6358-3.7425	0.2441	182	0.2046	3409	3591	100
3.7425-3.863	0.2341	190	0.1998	3401	3591	100
3.863-4.0007	0.2309	200	0.1946	3388	3588	100
4.0007-4.1604	0.2025	182	0.1846	3352	3534	100
4.1604-4.3491	0.2232	166	0.1785	3414	3580	100
4.3491-4.5775	0.1942	190	0.1764	3392	3582	100
4.5775-4.863	0.197	169	0.1776	3438	3607	100
4.863-5.2362	0.2153	179	0.1829	3391	3570	100
5.2362-5.7592	0.2281	178	0.1918	3406	3584	100
5.7592-6.5833	0.2396	183	0.2027	3413	3596	100
6.5833-8.2597	0.1904	175	0.1911	3451	3626	100
8.2597-28.2422	0.2277	190	0.2178	3478	3668	100

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Protein / Sugars , 2 types, 17 molecules GDEABCFHIJKLMNO

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