PDB-8xsu: Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Prot...

ID or keywords:

Entry

Database: PDB / ID: 8xsu

Title

Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Dinotefuran

Components

(Acetylcholine-binding protein) x 2

Keywords

SIGNALING PROTEIN / neonicotinoid / acetylcholine receptor

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: 2.632 Å

Authors

Ihara, M. / Okajima, T. / Matsuda, K.

Funding support

Japan, 2items

Citation

Journal: Open Biology / Year: 2024
Title: Unravelling nicotinic receptor and ligand features underlying neonicotinoid knockdown actions on the malaria vector mosquito Anopheles gambiae.
Authors: Ito, R. / Kamiya, M. / Takayama, K. / Mori, S. / Matsumoto, R. / Takebayashi, M. / Ojima, H. / Fujimura, S. / Yamamoto, H. / Ohno, M. / Ihara, M. / Okajima, T. / Yamashita, A. / Colman, F. / ...

History

Deposition	Jan 10, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 18, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8xsu.cif.gz	565.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8xsu.ent.gz		Display	PDB format
PDBx/mmJSON format	8xsu.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/xs/8xsu ftp://data.pdbj.org/pub/pdb/validation_reports/xs/8xsu	HTTPS FTP

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Related structure data

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 (6) #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

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: microscopy

Unit cell

Length a, b, c (Å)	74.149, 74.149, 350.306
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:
NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	ARG	ARG	0 - 206	1 - 207
2	1	1	SER	SER	ARG	ARG	0 - 206	1 - 207
3	2	2	LEU	LEU	SER	SER	1 - 207	2 - 208
4	2	2	LEU	LEU	SER	SER	1 - 207	2 - 208
5	3	3	LEU	LEU	GLY	GLY	1 - 205	2 - 206
6	3	3	LEU	LEU	GLY	GLY	1 - 205	2 - 206
7	4	4	SER	SER	ARG	ARG	0 - 206	1 - 207
8	4	4	SER	SER	ARG	ARG	0 - 206	1 - 207
9	5	5	LEU	LEU	ARG	ARG	1 - 206	2 - 207
10	5	5	LEU	LEU	ARG	ARG	1 - 206	2 - 207
11	6	6	LEU	LEU	GLY	GLY	1 - 205	2 - 206
12	6	6	LEU	LEU	GLY	GLY	1 - 205	2 - 206
13	7	7	SER	SER	SER	SER	0 - 207	1 - 208
14	7	7	SER	SER	SER	SER	0 - 207	1 - 208
15	8	8	LEU	LEU	GLY	GLY	1 - 205	2 - 206
16	8	8	LEU	LEU	GLY	GLY	1 - 205	2 - 206
17	9	9	LEU	LEU	ARG	ARG	1 - 206	2 - 207
18	9	9	LEU	LEU	ARG	ARG	1 - 206	2 - 207
19	10	10	LEU	LEU	GLY	GLY	1 - 205	2 - 206
20	10	10	LEU	LEU	GLY	GLY	1 - 205	2 - 206

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20

#1: Protein

Acetylcholine-binding protein / ACh-binding protein / AchBP

Mass: 23865.508 Da / Num. of mol.: 4 / Mutation: Q55R
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: Protein

Acetylcholine-binding protein / ACh-binding protein / AchBP

Mass: 23449.078 Da / Num. of mol.: 1 / Mutation: Q55R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Lymnaea stagnalis (great pond snail) / Production host:

Komagataella pastoris (fungus) / References: UniProt: P58154

#3: Chemical

ChemComp-A1LW0 / 2-methyl-1-nitro-3-[(tetrahydro-3-furanyl) methyl] guanidine / dinotefuran

Mass: 202.211 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₇H₁₄N₄O₃ / Feature type: SUBJECT OF INVESTIGATION

#4: 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

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

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.36 Å³/Da / Density % sol: 47.77 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4 / Details: PEG4000 16.5 - 18.0% , sodium citrate 0.2M

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL26B1 / Wavelength: 1 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 19, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.63→47.34 Å / Num. obs: 32196 / % possible obs: 99.9 % / Redundancy: 11.3 % / CC_1/2: 0.999 / R_merge(I) obs: 0.094 / R_pim(I) all: 0.043 / R_rim(I) all: 0.103 / Net I/σ(I): 22

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
8.73-47.34	10.5	0.025	915	1	0.012	0.027	99.2
2.63-2.76	11.3	0.827	4272	0.949	0.379	0.91	99.7

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Processing

Software

Name	Version	Classification
XDS	VERSION Jun 30, 2023 BUILT=20230630	data scaling
XDS	VERSION Jun 30, 2023 BUILT=20230630	data reduction
Aimless	version 0.7.9	data scaling
MOLREP	Vers 11.9.02; 28.02.2022	phasing
REFMAC	5.8.0419	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.632→47.34 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.919 / SU B: 34.119 / SU ML: 0.312 / Cross valid method: FREE R-VALUE / ESU R Free: 0.359
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2538	1629	5.077 %
R_work	0.1955	30460	-
all	0.198	-	-
obs	-	32089	99.888 %

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: 73.292 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.997 Å²	0.998 Å²	0 Å²
2-	-	1.997 Å²	-0 Å²
3-	-	-	-6.477 Å²

Refinement step

Cycle: LAST / Resolution: 2.632→47.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8285	0	140	48	8473

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	8628
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7883
X-RAY DIFFRACTION	r_angle_refined_deg	1.527	1.813	11772
X-RAY DIFFRACTION	r_angle_other_deg	0.542	1.768	18184
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.455	5	1039
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.556	5	95
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.771	10	1395
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.395	10	412
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1345
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10341
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2009
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	1274
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.199	0.2	7215
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	4193
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.099	0.2	4814
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.2	181
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.088	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.221	0.2	40
X-RAY DIFFRACTION	r_nbd_other	0.26	0.2	108
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.191	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	3.232	3.946	4159
X-RAY DIFFRACTION	r_mcbond_other	3.232	3.946	4159
X-RAY DIFFRACTION	r_mcangle_it	5.235	7.081	5191
X-RAY DIFFRACTION	r_mcangle_other	5.235	7.082	5192
X-RAY DIFFRACTION	r_scbond_it	3.519	4.317	4469
X-RAY DIFFRACTION	r_scbond_other	3.518	4.317	4470
X-RAY DIFFRACTION	r_scangle_it	5.647	7.752	6579
X-RAY DIFFRACTION	r_scangle_other	5.646	7.751	6580
X-RAY DIFFRACTION	r_lrange_it	8.904	42.106	8795
X-RAY DIFFRACTION	r_lrange_other	8.904	42.103	8794
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.094	0.05	6330
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.11	0.05	6241
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.115	0.05	6121
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.095	0.05	6333
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.109	0.05	6256
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.123	0.05	6078
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.102	0.05	6319
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.119	0.05	6126
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.114	0.05	6213
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.124	0.05	6079

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09408	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09408	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.10996	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.10996	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11516	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.11516	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.09482	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.09482	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.10866	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.10866	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.12329	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.12329	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.10153	0.05009
7	14	A	X-RAY DIFFRACTION	Local ncs	0.10153	0.05009
8	15	A	X-RAY DIFFRACTION	Local ncs	0.11857	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.11857	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.11408	0.05009
9	18	A	X-RAY DIFFRACTION	Local ncs	0.11408	0.05009
10	19	A	X-RAY DIFFRACTION	Local ncs	0.12375	0.05009
10	20	A	X-RAY DIFFRACTION	Local ncs	0.12375	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.632-2.7	0.393	112	0.323	2231	X-RAY DIFFRACTION	99.5327
2.7-2.774	0.344	107	0.299	2200	X-RAY DIFFRACTION	99.8269
2.774-2.854	0.353	115	0.266	2170	X-RAY DIFFRACTION	99.9563
2.854-2.941	0.306	145	0.266	1991	X-RAY DIFFRACTION	100
2.941-3.037	0.284	115	0.239	2002	X-RAY DIFFRACTION	100
3.037-3.144	0.28	125	0.226	1914	X-RAY DIFFRACTION	100
3.144-3.262	0.268	86	0.24	1891	X-RAY DIFFRACTION	100
3.262-3.394	0.316	97	0.234	1802	X-RAY DIFFRACTION	100
3.394-3.544	0.269	69	0.229	1752	X-RAY DIFFRACTION	100
3.544-3.716	0.273	100	0.236	1650	X-RAY DIFFRACTION	100
3.716-3.916	0.289	89	0.206	1583	X-RAY DIFFRACTION	100
3.916-4.152	0.236	74	0.17	1485	X-RAY DIFFRACTION	100
4.152-4.436	0.185	60	0.142	1404	X-RAY DIFFRACTION	100
4.436-4.788	0.189	79	0.131	1298	X-RAY DIFFRACTION	99.9274
4.788-5.239	0.159	59	0.129	1204	X-RAY DIFFRACTION	100
5.239-5.849	0.208	67	0.15	1078	X-RAY DIFFRACTION	99.9127
5.849-6.737	0.256	56	0.189	975	X-RAY DIFFRACTION	100
6.737-8.209	0.226	41	0.152	809	X-RAY DIFFRACTION	100
8.209-11.439	0.2	17	0.147	644	X-RAY DIFFRACTION	100
11.439-47.34	0.299	16	0.2	377	X-RAY DIFFRACTION	98.7437

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	1.9314	-0.4664	0.2889	2.4156	0.7615	6.8908	-0.044	0.0464	0.1614	0.0697	-0.0282	-0.1539	-0.554	0.6049	0.0721	0.0535	-0.0528	-0.0015	0.0578	0.0222	0.1237	-4.6729	-18.3584	0.883
2	2.2151	0.2144	0.4842	1.8057	0.8185	5.2159	-0.0405	0.0362	0.33	0.194	0.0913	0.2471	-0.7026	-0.8099	-0.0507	0.1554	0.1474	0.0285	0.1628	0.0663	0.2011	-31.3462	-13.1406	-0.0197
3	2.0212	0.0866	-0.2229	2.9605	-0.9663	4.851	-0.0721	0.1221	0.0225	0.0374	0.2246	0.3736	0.2654	-1.5861	-0.1525	0.0921	-0.1977	-0.0211	0.679	0.0633	0.2369	-44.2519	-36.5901	3.8496
4	3.2725	-0.0905	-0.1746	2.0484	0.1191	5.1338	-0.1493	0.095	-0.5733	-0.0805	0.0941	0.0881	1.2669	-0.5965	0.0552	0.5612	-0.2464	0.0081	0.1114	-0.0065	0.2534	-25.5766	-55.5383	7.838
5	1.6213	0.1137	-0.3585	2.0393	-0.8446	5.9168	-0.0763	0.0737	-0.2321	-0.0854	0.0034	-0.3682	0.7968	0.6128	0.0729	0.1361	0.0991	0.02	0.0892	0.0046	0.2314	-1.142	-44.5881	5.9163

Refinement TLS group

Selection: ALL

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