PDB-7pd6: Crystal structure of Lymnaea stagnalis Acetylcholine-binding prot...

ID or keywords:

Entry

Database: PDB / ID: 7pd6

Title

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

Components

Acetylcholine-binding protein

Keywords

CHOLINE-BINDING PROTEIN / acetylcholine / protein / mutant / SIGNALING PROTEIN

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 Å

Authors

Montgomery, M.G.

Funding support

United Kingdom, 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 4, 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 6, 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	7pd6.cif.gz	752.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7pd6.ent.gz		Display	PDB format
PDBx/mmJSON format	7pd6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7pd6_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	7pd6_full_validation.pdf.gz	2.8 MB	Display
Data in XML	7pd6_validation.xml.gz	70 KB	Display
Data in CIF	7pd6_validation.cif.gz	94.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pd/7pd6 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/7pd6	HTTPS FTP

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Related structure data

Related structure data	7pdbC 7pdrC 7pe5C 7pe6C 1uv6S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4zr6-d 3u8m-1 4zru-2 7pd6-2 5bp0-2 3u8m-3 7n0y-d 3wip-2 3u8n-3 5bp0-1 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

AaA: Acetylcholine-binding protein

BaB: Acetylcholine-binding protein

CaC: Acetylcholine-binding protein

DaD: Acetylcholine-binding protein

EaE: Acetylcholine-binding protein

FaF: Acetylcholine-binding protein

GaG: Acetylcholine-binding protein

HaH: Acetylcholine-binding protein

IaI: Acetylcholine-binding protein

JJJ: Acetylcholine-binding protein

hetero molecules

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

1

AaA: Acetylcholine-binding protein

BaB: Acetylcholine-binding protein

CaC: Acetylcholine-binding protein

DaD: Acetylcholine-binding protein

EaE: Acetylcholine-binding protein

hetero molecules

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

2

FaF: Acetylcholine-binding protein

GaG: Acetylcholine-binding protein

HaH: Acetylcholine-binding protein

IaI: Acetylcholine-binding protein

JJJ: 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)	115.886, 74.367, 130.058
Angle α, β, γ (deg.)	90.000, 101.645, 90.000
Int Tables number	3
Space group name H-M	P121

Noncrystallographic symmetry (NCS)

NCS domain:

#1: Protein	Acetylcholine-binding protein / ACh-binding protein / AchBP Mass: 23818.428 Da / Num. of mol.: 10 / Mutation: Q55R, D66N, 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-7II / Sulfoxaflor / [methyl-oxidanylidene-[1-[6-(trifluoromethyl)pyridin-3-yl]ethyl]-$l^{6}-sulfanylidene]cyanamide Mass: 277.266 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₁₀H₁₀F₃N₃OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.3 Å³/Da / Density % sol: 46.63 %
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: I24 / Wavelength: 0.96864 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96864 Å / Relative weight: 1
Reflection	Resolution: 1.796→127.381 Å / Num. obs: 117528 / % possible obs: 95 % / Redundancy: 6.7 % / CC_1/2: 0.997 / R_merge(I) obs: 0.11 / Net I/σ(I): 9.9
Reflection shell	Resolution: 1.796→2.034 Å / R_merge(I) obs: 1.097 / Num. unique obs: 5876 / CC_1/2: 0.613

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
STARANISO	2.3.20	data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1UV6

1uv6

Resolution: 2→127.381 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.931 / WR_factor R_free: 0.225 / WR_factor R_work: 0.202 / SU B: 12.457 / SU ML: 0.157 / Average fsc free: 0.8975 / Average fsc work: 0.9054 / Cross valid method: FREE R-VALUE / ESU R: 0.288 / ESU R Free: 0.2
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2311	5524	4.866 %
R_work	0.2063	107992	-
all	0.208	-	-
obs	-	113516	77.418 %

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: 38.199 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.233 Å²	-0 Å²	0.254 Å²
2-	-	0.054 Å²	-0 Å²
3-	-	-	0.991 Å²

Refinement step

Cycle: LAST / Resolution: 2→127.381 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15947	0	162	350	16459

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	16604
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	14961
X-RAY DIFFRACTION	r_angle_refined_deg	1.869	1.644	22714
X-RAY DIFFRACTION	r_angle_other_deg	1.364	1.575	34711
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.756	5	2013
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.961	21.525	938
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.726	15	2713
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.476	15	146
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	2250
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	18408
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3585
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	2400
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	13920
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	8060
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	8405
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	498
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.098	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.192	0.2	43
X-RAY DIFFRACTION	r_nbd_other	0.239	0.2	127
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.188	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	1.385	1.891	7992
X-RAY DIFFRACTION	r_mcbond_other	1.385	1.891	7991
X-RAY DIFFRACTION	r_mcangle_it	2.284	2.825	9962
X-RAY DIFFRACTION	r_mcangle_other	2.283	2.825	9963
X-RAY DIFFRACTION	r_scbond_it	2.019	2.163	8612
X-RAY DIFFRACTION	r_scbond_other	2.019	2.163	8613
X-RAY DIFFRACTION	r_scangle_it	3.341	3.153	12731
X-RAY DIFFRACTION	r_scangle_other	3.341	3.153	12732
X-RAY DIFFRACTION	r_lrange_it	5.532	21.539	17368
X-RAY DIFFRACTION	r_lrange_other	5.529	21.503	17343
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.096	0.05	6014
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.101	0.05	5990
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.089	0.05	6000
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.083	0.05	6063
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.071	0.05	6258
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.099	0.05	5969
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.094	0.05	5988
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.086	0.05	6045
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.085	0.05	6012
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.093	0.05	6236
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.102	0.05	6043
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.1	0.05	6116
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.106	0.05	6107
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.069	0.05	6339
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.093	0.05	6095
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.097	0.05	6091
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.099	0.05	6078
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.093	0.05	6085
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.092	0.05	6206
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.111	0.05	6043
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.088	0.05	6259
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.066	0.05	6307
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.092	0.05	6113
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.085	0.05	6139
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.081	0.05	6119
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.102	0.05	5970
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.091	0.05	6102
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.084	0.05	6112
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.05	0.05	6365
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.079	0.05	6146
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.098	0.05	6121
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.083	0.05	6218
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.08	0.05	6251
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.087	0.05	6154
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.065	0.05	6258
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.106	0.05	6007
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.105	0.05	6029
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.101	0.05	6029
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.096	0.05	6064
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.082	0.05	6167
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.094	0.05	6112
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.087	0.05	6085
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.092	0.05	6171
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.08	0.05	6182
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.085	0.05	6197

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
2-2.052	0.3	158	0.292	2919	0.293	10762	0.789	0.779	28.5913	0.283
2.052-2.108	0.27	200	0.283	4246	0.283	10499	0.832	0.816	42.3469	0.273
2.108-2.169	0.325	270	0.279	4955	0.282	10225	0.798	0.825	51.1002	0.264
2.169-2.236	0.291	257	0.264	5389	0.265	9928	0.84	0.854	56.8695	0.244
2.236-2.309	0.283	287	0.256	5773	0.257	9600	0.865	0.872	63.125	0.233
2.309-2.39	0.271	314	0.251	6277	0.252	9342	0.88	0.884	70.5523	0.225
2.39-2.481	0.28	337	0.251	6746	0.252	9006	0.859	0.884	78.6476	0.221
2.481-2.582	0.26	361	0.249	7105	0.25	8678	0.885	0.889	86.0336	0.223
2.582-2.697	0.286	378	0.241	7444	0.243	8317	0.878	0.894	94.0483	0.216
2.697-2.828	0.247	388	0.233	7481	0.234	7950	0.903	0.906	98.9811	0.208
2.828-2.981	0.254	345	0.218	7231	0.22	7578	0.91	0.923	99.9736	0.198
2.981-3.162	0.246	349	0.216	6773	0.217	7125	0.914	0.925	99.9579	0.201
3.162-3.38	0.227	300	0.206	6462	0.207	6770	0.928	0.94	99.8818	0.197
3.38-3.65	0.213	336	0.198	5948	0.199	6287	0.938	0.942	99.9523	0.197
3.65-3.999	0.225	289	0.181	5492	0.183	5784	0.941	0.955	99.9481	0.183
3.999-4.47	0.158	286	0.152	4971	0.152	5258	0.97	0.972	99.981	0.165
4.47-5.16	0.186	243	0.155	4422	0.156	4670	0.964	0.972	99.8929	0.173
5.16-6.318	0.225	202	0.177	3735	0.179	3947	0.957	0.966	99.7466	0.199
6.318-8.923	0.19	141	0.18	2932	0.18	3084	0.961	0.965	99.6433	0.209
8.923-127.381	0.3	83	0.247	1675	0.249	1768	0.962	0.961	99.4344	0.304

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	2.5467	-1.041	0.3207	2.4771	-0.0787	1.4626	0.0236	0.2586	0.0867	-0.4412	-0.1554	-0.43	0.0774	0.2864	0.1318	0.2872	0.0311	0.1192	0.123	0.071	0.1114	30.076	17.2057	22.3648
2	1.7849	-0.8769	-0.4628	3.0522	-0.0988	1.4206	0.0465	-0.0819	0.1783	0.266	-0.059	-0.3757	-0.105	0.1727	0.0126	0.1304	-0.0349	-0.0127	0.1232	0.0139	0.0591	32.0884	11.0476	48.438
3	3.4603	-0.6175	0.5065	2.0713	-0.0367	0.8462	0.0292	-0.1484	-0.0539	0.1621	-0.0038	0.1085	0.1003	-0.0587	-0.0253	0.1347	-0.0204	-0.0017	0.0852	0.0262	0.0143	18.1787	-11.689	52.6133
4	1.6168	-1.1756	-0.1591	2.2207	-0.3108	0.7071	0.0809	0.0989	-0.136	-0.3959	-0.0384	0.2236	0.1357	-0.0775	-0.0425	0.2987	-0.021	-0.1045	0.092	0.0049	0.1018	7.6567	-19.0016	29.3198
5	1.926	-0.4773	-0.2473	2.9955	-0.1014	1.2214	0.0516	0.3074	0.086	-0.8093	-0.065	0.1016	0.24	0.1103	0.0134	0.5828	0.0323	-0.054	0.174	0.0234	0.0306	15.5687	-1.4721	10.9318
6	2.5293	0.9451	-0.1634	2.2142	-0.7079	1.4425	-0.0853	-0.013	0.1705	0.0281	0.0536	0.297	-0.148	-0.2152	0.0317	0.1787	0.0428	-0.0245	0.0655	-0.0387	0.0732	-45.3287	54.6651	42.1959
7	2.0736	0.5847	-0.1538	2.7314	0.7255	1.7385	-0.0699	0.2235	0.2323	-0.4062	-0.0187	0.2149	-0.2271	-0.1957	0.0885	0.3127	0.0163	-0.1145	0.186	0.0337	0.0658	-45.6876	48.5198	16.1681
8	3.1082	0.4539	0.9743	1.6822	-0.1005	1.2965	0.0152	0.272	-0.2062	-0.2369	-0.0459	-0.1677	0.0515	0.1496	0.0307	0.2408	0.003	-0.0019	0.1992	-0.0133	0.034	-31.9813	25.7647	12.7012
9	2.1316	1.0572	-0.0698	1.5414	0.1807	1.0333	-0.0043	-0.0199	-0.0943	0.0584	0.0211	-0.1182	0.1648	0.1537	-0.0168	0.1961	0.0352	-0.0249	0.0814	-0.0112	0.105	-22.4037	18.3319	36.2929
10	2.0974	0.335	-0.1013	2.2259	-0.2424	0.6785	-0.0807	-0.1874	0.014	0.2015	-0.0054	-0.125	-0.0134	0.0048	0.0861	0.1975	0.0207	-0.0375	0.0657	-0.0051	0.0193	-31.0783	36.1233	54.2715

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	0 - 204
2	X-RAY DIFFRACTION	2	ALL	BBB	0 - 204
3	X-RAY DIFFRACTION	3	ALL	CCC	0 - 204
4	X-RAY DIFFRACTION	4	ALL	DDD	0 - 207
5	X-RAY DIFFRACTION	5	ALL	EEE	0 - 204
6	X-RAY DIFFRACTION	6	ALL	FFF	0 - 204
7	X-RAY DIFFRACTION	7	ALL	GGG	0 - 204
8	X-RAY DIFFRACTION	8	ALL	HHH	0 - 204
9	X-RAY DIFFRACTION	9	ALL	III	0 - 207
10	X-RAY DIFFRACTION	10	ALL	JJJ	2 - 204

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About Yorodumi

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Yorodumi