PDB-7pe6: Crystal structure of Lymnaea stagnalis Acetylcholine-binding prot...

ID or keywords:

Entry

Database: PDB / ID: 7pe6

Title

Crystal structure of Lymnaea stagnalis Acetylcholine-binding protein (Ls-AChBP) Q55R/M114V double mutant complexed with Flupyrimin

Components

Acetylcholine-binding protein

Keywords

SIGNALING PROTEIN / Acetylcholine / protein / insecticide

Function / homology

Function and homology information

synaptic cleft / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / synapse / membrane
Similarity search - Function

Biological species

Lymnaea stagnalis (great pond snail)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.01 Å

Authors

Montgomery, M.G.

Funding support

1items

Citation

Journal: J.Med.Chem. / Year: 2022
Title: Structural Biology-Guided Design, Synthesis, and Biological Evaluation of Novel Insect Nicotinic Acetylcholine Receptor Orthosteric Modulators.
Authors: Montgomery, M. / Rendine, S. / Zimmer, C.T. / Elias, J. / Schaetzer, J. / Pitterna, T. / Benfatti, F. / Skaljac, M. / Bigot, A.

History

Deposition	Aug 9, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 23, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7pe6.cif.gz	389.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7pe6.ent.gz		Display	PDB format
PDBx/mmJSON format	7pe6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7pe6_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	7pe6_full_validation.pdf.gz	2.6 MB	Display
Data in XML	7pe6_validation.xml.gz	35.1 KB	Display
Data in CIF	7pe6_validation.cif.gz	48.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pe/7pe6 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/7pe6	HTTPS FTP

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Related structure data

Related structure data	7pd6C 7pdbC 7pdrC 7pe5C 1uv6S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3zdg-4 7pe5-d 7pd6-2 3zdg-2 4alx-1 4um3-7 3zdh-1 3u8m-3 4um3-2 3u8l-1 4um3-8 3zdh-2 4um3-4 5y2q-d 3u8m-2 3u8m-4 4um3-1 3u8j-2 4alx-2 3u8n-4 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

AaA: Acetylcholine-binding protein

BaB: Acetylcholine-binding protein

CaC: Acetylcholine-binding protein

DaD: Acetylcholine-binding protein

EaE: Acetylcholine-binding protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	74.040, 74.040, 350.590
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains AAA BBB
2	1	Chains AAA CCC
3	1	Chains AAA DDD
4	1	Chains AAA EEE
5	1	Chains BBB CCC
6	1	Chains BBB DDD
7	1	Chains BBB EEE
8	1	Chains CCC DDD
9	1	Chains CCC EEE
10	1	Chains DDD EEE

#1: Protein	Acetylcholine-binding protein / ACh-binding protein / AchBP Mass: 23818.428 Da / Num. of mol.: 5 / Mutation: Q55R, N66D, M114V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Production host: Komagataella pastoris (fungus) / References: UniProt: P58154
#2: Chemical	ChemComp-7OF / (~{N}~{E})-~{N}-[1-[(6-chloranylpyridin-3-yl)methyl]pyridin-2-ylidene]-2,2,2-tris(fluoranyl)ethanamide Mass: 315.678 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₃H₉ClF₃N₃O / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.32 Å³/Da / Density % sol: 46.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 14-18% PEG3350, 0.1-0.25M diammonium hydrogen citrate, 15% glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.01→64.121 Å / Num. obs: 71932 / % possible obs: 99.9 % / Redundancy: 7.5 % / R_merge(I) obs: 0.072 / R_pim(I) all: 0.03 / R_rim(I) all: 0.084 / Net I/σ(I): 13.6
Reflection shell	Resolution: 2.01→2.06 Å / Redundancy: 7.8 % / R_merge(I) obs: 0.656 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5333 / R_pim(I) all: 0.27 / R_rim(I) all: 0.755 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1UV6

1uv6

Resolution: 2.01→64.121 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.951 / WR_factor R_free: 0.241 / WR_factor R_work: 0.201 / SU B: 12.28 / SU ML: 0.145 / Average fsc free: 0.895 / Average fsc work: 0.9022 / Cross valid method: FREE R-VALUE / ESU R: 0.189 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2269	3542	4.934 %
R_work	0.1907	68249	-
all	0.192	-	-
obs	-	71791	99.908 %

Solvent computation

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

Displacement parameters

B_iso mean: 56.849 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.18 Å²	0.59 Å²	-0 Å²
2-	-	1.18 Å²	0 Å²
3-	-	-	-3.827 Å²

Refinement step

Cycle: LAST / Resolution: 2.01→64.121 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7978	0	105	112	8195

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	8328
X-RAY DIFFRACTION	r_bond_other_d	0.035	0.017	7442
X-RAY DIFFRACTION	r_angle_refined_deg	1.775	1.622	11376
X-RAY DIFFRACTION	r_angle_other_deg	2.353	1.567	17253
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.152	5	990
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.127	21.577	463
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.714	15	1339
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.65	15	71
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	1113
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	9242
X-RAY DIFFRACTION	r_gen_planes_other	0.014	0.02	1812
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	1314
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.218	0.2	6761
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	4003
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	3808
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	224
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.157	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.231	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.315	0.2	61
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.139	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	2.584	3.226	3984
X-RAY DIFFRACTION	r_mcbond_other	2.584	3.226	3982
X-RAY DIFFRACTION	r_mcangle_it	3.823	4.817	4963
X-RAY DIFFRACTION	r_mcangle_other	3.823	4.817	4963
X-RAY DIFFRACTION	r_scbond_it	3.595	3.73	4344
X-RAY DIFFRACTION	r_scbond_other	3.595	3.73	4345
X-RAY DIFFRACTION	r_scangle_it	5.519	5.418	6412
X-RAY DIFFRACTION	r_scangle_other	5.519	5.418	6413
X-RAY DIFFRACTION	r_lrange_it	8.949	37.509	8795
X-RAY DIFFRACTION	r_lrange_other	8.972	37.433	8784
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	6072
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.099	0.05	6058
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.092	0.05	6146
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.1	0.05	6113
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.086	0.05	6078
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.091	0.05	6108
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.09	0.05	6124
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.084	0.05	6102
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.078	0.05	6133
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.091	0.05	6095

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.01-2.062	0.268	247	0.286	5079	0.285	5330	0.789	0.762	99.9249	0.248
2.062-2.119	0.253	228	0.263	4944	0.262	5179	0.831	0.827	99.8648	0.229
2.119-2.18	0.286	278	0.244	4770	0.246	5049	0.828	0.857	99.9802	0.213
2.18-2.247	0.258	273	0.232	4613	0.233	4887	0.887	0.884	99.9795	0.205
2.247-2.321	0.247	246	0.222	4469	0.224	4715	0.901	0.901	100	0.198
2.321-2.402	0.284	221	0.228	4328	0.231	4550	0.886	0.906	99.978	0.207
2.402-2.492	0.25	183	0.218	4231	0.22	4414	0.906	0.916	100	0.2
2.492-2.594	0.263	210	0.214	4041	0.216	4251	0.916	0.923	100	0.199
2.594-2.709	0.245	188	0.209	3895	0.211	4083	0.918	0.927	100	0.199
2.709-2.841	0.235	209	0.214	3734	0.215	3944	0.921	0.929	99.9746	0.207
2.841-2.995	0.277	157	0.207	3525	0.21	3682	0.893	0.922	100	0.206
2.995-3.176	0.272	193	0.213	3303	0.216	3496	0.895	0.921	100	0.219
3.176-3.394	0.262	162	0.214	3152	0.217	3316	0.915	0.93	99.9397	0.224
3.394-3.666	0.228	164	0.195	2906	0.196	3074	0.932	0.945	99.8699	0.209
3.666-4.014	0.211	148	0.181	2672	0.183	2823	0.947	0.95	99.8937	0.197
4.014-4.486	0.177	149	0.139	2384	0.141	2548	0.967	0.973	99.4113	0.162
4.486-5.175	0.18	96	0.144	2164	0.145	2273	0.967	0.973	99.4281	0.167
5.175-6.328	0.206	86	0.177	1828	0.179	1922	0.948	0.957	99.5838	0.205
6.328-8.906	0.196	69	0.155	1411	0.156	1484	0.956	0.971	99.7305	0.181
8.906-64.121	0.203	35	0.188	801	0.189	838	0.963	0.961	99.7613	0.219

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.8528	0.1791	-0.1768	0.8392	-0.2294	1.9948	0.0993	0.0056	-0.2269	-0.0897	-0.0104	-0.0541	0.5682	0.2319	-0.089	0.2818	0.061	-0.0187	0.2303	0.0325	0.1921	46.9358	-20.192	2.0475
2	0.7164	-0.3947	0.0211	0.8585	-0.4069	1.9541	0.0212	0.0611	-0.2129	-0.0744	0.1535	0.2045	0.5783	-0.3633	-0.1747	0.2218	-0.1995	-0.0534	0.3435	0.0608	0.216	20.5487	-19.1108	-1.4454
3	0.7346	0.4084	-0.2124	1.7354	-0.0676	2.3213	0.0296	-0.0376	0.1771	-0.0308	0.0443	0.4891	-0.126	-0.8016	-0.0739	0.0155	0.0644	-0.0128	0.4668	0.0683	0.2585	13.7211	6.4309	-5.5089
4	0.9499	-0.1717	0.432	0.5672	-0.1762	2.2172	-0.0648	-0.1127	0.2873	0.0695	0.0457	0.1199	-0.5923	-0.1407	0.0191	0.3502	0.0464	-0.03	0.1815	0.0068	0.2304	35.4534	21.4868	-3.7173
5	0.7319	-0.2588	0.0249	1.2022	-0.0929	2.5976	0.0027	0.0603	0.0543	0.0418	-0.0529	-0.1216	-0.1746	0.4873	0.0501	0.1583	-0.061	-0.0175	0.3741	0.0228	0.2013	55.951	5.0421	1.0504

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AaA	1 - 204
2	X-RAY DIFFRACTION	2	ALL	BaB	1 - 207
3	X-RAY DIFFRACTION	3	ALL	CaC	1 - 204
4	X-RAY DIFFRACTION	4	ALL	DaD	1 - 204
5	X-RAY DIFFRACTION	5	ALL	EaE	1 - 205

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