PDB-6sgv: Crystal structure of AcAChBP in complex with hosieine

ID or keywords:

Entry

Database: PDB / ID: 6sgv

Title

Crystal structure of AcAChBP in complex with hosieine

Components

Soluble acetylcholine receptor

Keywords

SIGNALING PROTEIN / toxin / acetylcholine binding protein

Function / homology

Function and homology information

extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding
Similarity search - Function

Biological species

Aplysia californica (California sea hare)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.6 Å

Authors

Hunter, W.N. / Dawson, A. / Parker, H.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Delineating the activity of the potent nicotinic acetylcholine receptor agonists (+)-anatoxin-a and (-)-hosieine-A
Authors: Parker, H.P. / Dawson, A. / Jones, M.J. / Yan, R. / Ouyang, J. / Hong, R. / Hunter, W.N.

History

Deposition	Aug 5, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 26, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 7, 2022	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 13, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _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	6sgv.cif.gz	420.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6sgv.ent.gz	344.3 KB	Display	PDB format
PDBx/mmJSON format	6sgv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sg/6sgv ftp://data.pdbj.org/pub/pdb/validation_reports/sg/6sgv	HTTPS FTP

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Related structure data

Related structure data	6sh0C C: citing same article (ref.)
Similar structure data	4bqt-d 6sh0-2 6qkk-2 6qkk-1 6qqo-1 5oa0-d 6sh0-1 5o87-2 2y54-d 2y58-d 6qqo-2 5oal-2 4aft-d 5obg-d 5lxb-2 5obh-d 6qqp-2 5lxb-1 2y57-d 5oan-d 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

6sh0C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (4) #71 - Nov 2005 Acetylcholine Receptor similarity (4)

Deposited unit

A: Soluble acetylcholine receptor

B: Soluble acetylcholine receptor

C: Soluble acetylcholine receptor

D: Soluble acetylcholine receptor

E: Soluble acetylcholine receptor

F: Soluble acetylcholine receptor

G: Soluble acetylcholine receptor

H: Soluble acetylcholine receptor

I: Soluble acetylcholine receptor

J: Soluble acetylcholine receptor

hetero molecules

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

1

A: Soluble acetylcholine receptor

B: Soluble acetylcholine receptor

C: Soluble acetylcholine receptor

D: Soluble acetylcholine receptor

E: Soluble acetylcholine receptor

hetero molecules

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

2

F: Soluble acetylcholine receptor

G: Soluble acetylcholine receptor

H: Soluble acetylcholine receptor

I: Soluble acetylcholine receptor

J: Soluble acetylcholine receptor

hetero molecules

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

Unit cell

Length a, b, c (Å)	209.802, 133.414, 131.155
Angle α, β, γ (deg.)	90.000, 102.510, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

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	ARG	ARG	A	A	20 - 224	20 - 224
2	1	ARG	ARG	B	B	20 - 224	20 - 224
1	2	ARG	ARG	A	A	20 - 224	20 - 224
2	2	ARG	ARG	C	C	20 - 224	20 - 224
1	3	ARG	ARG	A	A	20 - 224	20 - 224
2	3	ARG	ARG	D	D	20 - 224	20 - 224
1	4	ARG	ARG	A	A	20 - 224	20 - 224
2	4	ARG	ARG	E	E	20 - 224	20 - 224
1	5	ARG	ARG	A	A	20 - 224	20 - 224
2	5	ARG	ARG	F	F	20 - 224	20 - 224
1	6	ARG	ARG	A	A	20 - 224	20 - 224
2	6	ARG	ARG	G	G	20 - 224	20 - 224
1	7	GLU	GLU	A	A	20 - 223	20 - 223
2	7	GLU	GLU	H	H	20 - 223	20 - 223
1	8	ARG	ARG	A	A	20 - 224	20 - 224
2	8	ARG	ARG	I	I	20 - 224	20 - 224
1	9	ARG	ARG	A	A	20 - 224	20 - 224
2	9	ARG	ARG	J	J	20 - 224	20 - 224
1	10	ARG	ARG	B	B	20 - 224	20 - 224
2	10	ARG	ARG	C	C	20 - 224	20 - 224
1	11	ARG	ARG	B	B	20 - 224	20 - 224
2	11	ARG	ARG	D	D	20 - 224	20 - 224
1	12	ARG	ARG	B	B	20 - 224	20 - 224
2	12	ARG	ARG	E	E	20 - 224	20 - 224
1	13	ARG	ARG	B	B	20 - 224	20 - 224
2	13	ARG	ARG	F	F	20 - 224	20 - 224
1	14	ARG	ARG	B	B	20 - 224	20 - 224
2	14	ARG	ARG	G	G	20 - 224	20 - 224
1	15	GLU	GLU	B	B	20 - 223	20 - 223
2	15	GLU	GLU	H	H	20 - 223	20 - 223
1	16	ARG	ARG	B	B	20 - 224	20 - 224
2	16	ARG	ARG	I	I	20 - 224	20 - 224
1	17	ARG	ARG	B	B	20 - 224	20 - 224
2	17	ARG	ARG	J	J	20 - 224	20 - 224
1	18	ARG	ARG	C	C	20 - 224	20 - 224
2	18	ARG	ARG	D	D	20 - 224	20 - 224
1	19	ARG	ARG	C	C	20 - 224	20 - 224
2	19	ARG	ARG	E	E	20 - 224	20 - 224
1	20	ARG	ARG	C	C	20 - 224	20 - 224
2	20	ARG	ARG	F	F	20 - 224	20 - 224
1	21	ARG	ARG	C	C	20 - 224	20 - 224
2	21	ARG	ARG	G	G	20 - 224	20 - 224
1	22	GLU	GLU	C	C	20 - 223	20 - 223
2	22	GLU	GLU	H	H	20 - 223	20 - 223
1	23	ARG	ARG	C	C	20 - 224	20 - 224
2	23	ARG	ARG	I	I	20 - 224	20 - 224
1	24	ARG	ARG	C	C	20 - 224	20 - 224
2	24	ARG	ARG	J	J	20 - 224	20 - 224
1	25	ARG	ARG	D	D	20 - 224	20 - 224
2	25	ARG	ARG	E	E	20 - 224	20 - 224
1	26	ARG	ARG	D	D	20 - 224	20 - 224
2	26	ARG	ARG	F	F	20 - 224	20 - 224
1	27	ARG	ARG	D	D	20 - 224	20 - 224
2	27	ARG	ARG	G	G	20 - 224	20 - 224
1	28	GLU	GLU	D	D	20 - 223	20 - 223
2	28	GLU	GLU	H	H	20 - 223	20 - 223
1	29	ARG	ARG	D	D	20 - 224	20 - 224
2	29	ARG	ARG	I	I	20 - 224	20 - 224
1	30	ARG	ARG	D	D	20 - 224	20 - 224
2	30	ARG	ARG	J	J	20 - 224	20 - 224
1	31	ARG	ARG	E	E	20 - 224	20 - 224
2	31	ARG	ARG	F	F	20 - 224	20 - 224
1	32	ARG	ARG	E	E	20 - 224	20 - 224
2	32	ARG	ARG	G	G	20 - 224	20 - 224
1	33	GLU	GLU	E	E	20 - 223	20 - 223
2	33	GLU	GLU	H	H	20 - 223	20 - 223
1	34	ARG	ARG	E	E	20 - 224	20 - 224
2	34	ARG	ARG	I	I	20 - 224	20 - 224
1	35	ARG	ARG	E	E	20 - 224	20 - 224
2	35	ARG	ARG	J	J	20 - 224	20 - 224
1	36	ARG	ARG	F	F	20 - 224	20 - 224
2	36	ARG	ARG	G	G	20 - 224	20 - 224
1	37	GLU	GLU	F	F	20 - 223	20 - 223
2	37	GLU	GLU	H	H	20 - 223	20 - 223
1	38	ARG	ARG	F	F	20 - 224	20 - 224
2	38	ARG	ARG	I	I	20 - 224	20 - 224
1	39	ARG	ARG	F	F	20 - 224	20 - 224
2	39	ARG	ARG	J	J	20 - 224	20 - 224
1	40	GLU	GLU	G	G	20 - 223	20 - 223
2	40	GLU	GLU	H	H	20 - 223	20 - 223
1	41	ARG	ARG	G	G	20 - 224	20 - 224
2	41	ARG	ARG	I	I	20 - 224	20 - 224
1	42	ARG	ARG	G	G	20 - 224	20 - 224
2	42	ARG	ARG	J	J	20 - 224	20 - 224
1	43	GLU	GLU	H	H	20 - 223	20 - 223
2	43	GLU	GLU	I	I	20 - 223	20 - 223
1	44	GLU	GLU	H	H	20 - 223	20 - 223
2	44	GLU	GLU	J	J	20 - 223	20 - 223
1	45	ARG	ARG	I	I	20 - 224	20 - 224
2	45	ARG	ARG	J	J	20 - 224	20 - 224

NCS ensembles :

#1: Protein

Soluble acetylcholine receptor

Mass: 28326.750 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Aplysia californica (California sea hare)
Cell line (production host): Sf9 / Production host:

Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WSF8

#2: 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.: 3
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

#3: Chemical

ChemComp-LDQ / Hosieine

Mass: 244.332 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₁₅H₂₀N₂O / Feature type: SUBJECT OF INVESTIGATION

#4: Chemical

ChemComp-ACT / ACETATE ION

Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 434 / 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: 3.84 Å³/Da / Density % sol: 68 % / Description: prism
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: reservoir solution: 0.2 M CaCl2, 0.1M NaOAc pH 4.5, 16% isopropanol Protein buffer: 50 mM tris pH 7.5, 250 mM NaCl, 4 mg/ml mixed in 1ul protein : 2 ul reservoir

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 19, 2018
Radiation	Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.6→45.03 Å / Num. obs: 108313 / % possible obs: 100 % / Redundancy: 6.3 % / B_iso Wilson estimate: 14.5 Å² / CC_1/2: 0.986 / R_merge(I) obs: 0.24 / R_pim(I) all: 0.104 / R_rim(I) all: 0.261 / Net I/σ(I): 6
Reflection shell	Resolution: 2.6→2.64 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.96 / Num. unique obs: 5354 / CC_1/2: 0.776 / R_pim(I) all: 0.418 / R_rim(I) all: 1.048 / % possible all: 99.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.5.32	data scaling
MOLREP		phasing
REFMAC	5.8.0189	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→45.03 Å / Cor.coef. F_o:F_c: 0.911 / Cor.coef. F_o:F_c free: 0.889 / SU B: 9.588 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.433 / ESU R Free: 0.277
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.257	5457	5 %	RANDOM
R_work	0.2323	-	-	-
obs	0.2335	102825	99.92 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 106.85 Å² / B_iso mean: 28.07 Å² / B_iso min: 0.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.58 Å²	0 Å²	-0.86 Å²
2-	-	2.94 Å²	0 Å²
3-	-	-	-0.89 Å²

Refinement step

Cycle: final / Resolution: 2.6→45.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16371	0	226	434	17031
B_iso mean	-	-	32.63	19.88	-
Num. residues	-	-	-	-	2051

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.02	17109
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	15191
X-RAY DIFFRACTION	r_angle_refined_deg	1.538	1.95	23408
X-RAY DIFFRACTION	r_angle_other_deg	0.938	3	35395
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.026	5	2051
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.65	24.411	798
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.498	15	2744
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.757	15	98
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	2648
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	19188
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3472

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	12996	0.04
1	2	B	12996	0.04
2	1	A	13034	0.03
2	2	C	13034	0.03
3	1	A	13008	0.03
3	2	D	13008	0.03
4	1	A	13008	0.04
4	2	E	13008	0.04
5	1	A	12998	0.03
5	2	F	12998	0.03
6	1	A	12944	0.04
6	2	G	12944	0.04
7	1	A	12906	0.04
7	2	H	12906	0.04
8	1	A	12996	0.04
8	2	I	12996	0.04
9	1	A	12990	0.04
9	2	J	12990	0.04
10	1	B	13058	0.03
10	2	C	13058	0.03
11	1	B	13056	0.04
11	2	D	13056	0.04
12	1	B	13046	0.03
12	2	E	13046	0.03
13	1	B	12894	0.04
13	2	F	12894	0.04
14	1	B	13056	0.02
14	2	G	13056	0.02
15	1	B	12934	0.03
15	2	H	12934	0.03
16	1	B	13012	0.04
16	2	I	13012	0.04
17	1	B	13026	0.03
17	2	J	13026	0.03
18	1	C	13124	0.03
18	2	D	13124	0.03
19	1	C	13126	0.03
19	2	E	13126	0.03
20	1	C	12990	0.04
20	2	F	12990	0.04
21	1	C	13034	0.04
21	2	G	13034	0.04
22	1	C	13034	0.03
22	2	H	13034	0.03
23	1	C	13060	0.04
23	2	I	13060	0.04
24	1	C	13106	0.03
24	2	J	13106	0.03
25	1	D	13126	0.04
25	2	E	13126	0.04
26	1	D	13022	0.04
26	2	F	13022	0.04
27	1	D	13086	0.04
27	2	G	13086	0.04
28	1	D	13000	0.03
28	2	H	13000	0.03
29	1	D	13138	0.03
29	2	I	13138	0.03
30	1	D	13100	0.04
30	2	J	13100	0.04
31	1	E	12938	0.04
31	2	F	12938	0.04
32	1	E	13012	0.04
32	2	G	13012	0.04
33	1	E	12982	0.03
33	2	H	12982	0.03
34	1	E	13030	0.04
34	2	I	13030	0.04
35	1	E	13078	0.03
35	2	J	13078	0.03
36	1	F	12906	0.05
36	2	G	12906	0.05
37	1	F	12902	0.04
37	2	H	12902	0.04
38	1	F	12932	0.05
38	2	I	12932	0.05
39	1	F	12958	0.04
39	2	J	12958	0.04
40	1	G	12864	0.04
40	2	H	12864	0.04
41	1	G	12960	0.04
41	2	I	12960	0.04
42	1	G	12970	0.03
42	2	J	12970	0.03
43	1	H	12976	0.04
43	2	I	12976	0.04
44	1	H	12966	0.03
44	2	J	12966	0.03
45	1	I	13054	0.04
45	2	J	13054	0.04

LS refinement shell

Resolution: 2.6→2.668 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.331	407	-
R_work	0.291	7547	-
all	-	7954	-
obs	-	-	99.94 %

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Jul 12, 2017. Major update of PDB

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Yorodumi