PDB-2ph9: Galanthamine bound to an ACh-binding Protein

ID or keywords:

Entry

Database: PDB / ID: 2ph9

Title

Galanthamine bound to an ACh-binding Protein

Components

Soluble acetylcholine receptor

Keywords

CHOLINE-BINDING PROTEIN / non-competitive inhibitors / nicotinic acetylcholine receptor / acetylcholine-binding protein / benzodiazepine / galanthamine

Function / homology

Function and homology information

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

Biological species

Aplysia californica (California sea hare)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.88 Å

Authors

Hansen, S.B. / Taylor, P.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: Galanthamine and non-competitive inhibitor binding to ACh-binding protein: evidence for a binding site on non-alpha-subunit interfaces of heteromeric neuronal nicotinic receptors.
Authors: Hansen, S.B. / Taylor, P.

History

Deposition	Apr 10, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 3, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.4	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2ph9.cif.gz	223.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2ph9.ent.gz	181.1 KB	Display	PDB format
PDBx/mmJSON format	2ph9.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2ph9_validation.pdf.gz	3.5 MB	Display	wwPDB validaton report
Full document	2ph9_full_validation.pdf.gz	3.5 MB	Display
Data in XML	2ph9_validation.xml.gz	44.1 KB	Display
Data in CIF	2ph9_validation.cif.gz	56.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ph/2ph9 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/2ph9	HTTPS FTP

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Related structure data

Related structure data	2pgzC 2bynS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2byn-d 2x00-d 3t4m-2 3t4m-1 3pmz-1 4xhe-1 5brx-2 5tvh-d 2byr-1 5tsf-d 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	#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

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	143.950, 145.472, 143.555
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	E-302- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	ARG	ARG	E	E	200 - 208	209 - 217
2	1	LEU	LEU	ARG	ARG	B	B	200 - 208	209 - 217
3	1	LEU	LEU	ARG	ARG	C	C	200 - 208	209 - 217
4	1	LEU	LEU	ARG	ARG	D	D	200 - 208	209 - 217
5	1	LEU	LEU	ARG	ARG	A	A	200 - 208	209 - 217
1	2	ASP	ASP	PHE	PHE	A	A	-5 - 14	4 - 23
2	2	TYR	TYR	PHE	PHE	B	B	-7 - 14	2 - 23
3	2	ASP	ASP	PHE	PHE	C	C	-5 - 14	4 - 23
4	2	ASP	ASP	PHE	PHE	D	D	-5 - 14	4 - 23
5	2	ASP	ASP	PHE	PHE	E	E	-4 - 14	5 - 23
1	3	TYR	TYR	VAL	VAL	A	A	20 - 185	29 - 194
2	3	TYR	TYR	VAL	VAL	B	B	20 - 185	29 - 194
3	3	TYR	TYR	VAL	VAL	C	C	20 - 185	29 - 194
4	3	TYR	TYR	VAL	VAL	D	D	20 - 185	29 - 194
5	3	TYR	TYR	VAL	VAL	E	E	20 - 185	29 - 194
1	4	GNT	GNT	GNT	GNT	C	H	301
2	4	GNT	GNT	GNT	GNT	A	F	301
3	4	GNT	GNT	GNT	GNT	E	J	301
4	4	GNT	GNT	GNT	GNT	D	I	301

NCS ensembles :

ID
1
2
3
4

#1: Protein	Soluble acetylcholine receptor Mass: 26212.105 Da / Num. of mol.: 5 / Fragment: residues 18-236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aplysia californica (California sea hare) Gene: synthetic gene / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Chemical	ChemComp-GNT / (-)-GALANTHAMINE Mass: 287.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₁NO₃
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H₂O
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: 2.87 Å³/Da / Density % sol: 57.08 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M sodium citrate, 10% (w/v) PEG-1000, 24% (v/v) isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 31, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.85→50 Å / Num. all: 33957 / Num. obs: 33957 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / B_iso Wilson estimate: 57.4 Å² / R_merge(I) obs: 0.14 / Χ²: 1.047 / Net I/σ(I): 8.5
Reflection shell	Resolution: 2.85→2.95 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.535 / Mean I/σ(I) obs: 14.7 / Num. unique all: 3374 / Χ²: 1.136 / % possible all: 100

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Phasing

Phasing MR

R_factor: 0.306 / Cor.coef. F_o:F_c: 0.8 / Cor.coef. Io to Ic: 0.793

	Highest resolution	Lowest resolution
Rotation	3 Å	15 Å
Translation	3 Å	15 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	2	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2BYN

2byn

Resolution: 2.88→20 Å / Cor.coef. F_o:F_c: 0.923 / Cor.coef. F_o:F_c free: 0.893 / SU B: 28.128 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.237	1714	5.1 %	RANDOM
R_work	0.205	-	-	-
obs	0.207	33817	98.8 %	-
all	-	33957	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 39.971 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.44 Å²	0 Å²	0 Å²
2-	-	0.98 Å²	0 Å²
3-	-	-	-0.55 Å²

Refinement step

Cycle: LAST / Resolution: 2.88→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8527	0	97	104	8728

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	8942
X-RAY DIFFRACTION	r_angle_refined_deg	1.525	1.976	12217
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.43	5	1060
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.332	24.599	424
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.508	15	1423
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	27.657	15	50
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	1355
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	6827
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	3469
X-RAY DIFFRACTION	r_nbtor_refined	0.318	0.2	6134
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	331
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.462	0.2	44
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.416	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	0.629	1.5	5438
X-RAY DIFFRACTION	r_mcangle_it	1.061	2	8733
X-RAY DIFFRACTION	r_scbond_it	1.401	3	4023
X-RAY DIFFRACTION	r_scangle_it	2.396	4.5	3484

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	E	83	TIGHT POSITIONAL	0.06	0.05
1	2	B	83	TIGHT POSITIONAL	0.12	0.05
1	3	C	83	TIGHT POSITIONAL	0.06	0.05
1	4	D	83	TIGHT POSITIONAL	0.12	0.05
1	5	A	83	TIGHT POSITIONAL	0.05	0.05
1	1	E	83	TIGHT THERMAL	0.09	0.5
1	2	B	83	TIGHT THERMAL	0.06	0.5
1	3	C	83	TIGHT THERMAL	0.06	0.5
1	4	D	83	TIGHT THERMAL	0.07	0.5
1	5	A	83	TIGHT THERMAL	0.08	0.5
2	1	A	148	TIGHT POSITIONAL	0.04	0.05
2	2	B	148	TIGHT POSITIONAL	0.04	0.05
2	3	C	148	TIGHT POSITIONAL	0.04	0.05
2	4	D	148	TIGHT POSITIONAL	0.04	0.05
2	5	E	148	TIGHT POSITIONAL	0.09	0.05
2	1	A	148	TIGHT THERMAL	0.06	0.5
2	2	B	148	TIGHT THERMAL	0.07	0.5
2	3	C	148	TIGHT THERMAL	0.06	0.5
2	4	D	148	TIGHT THERMAL	0.06	0.5
2	5	E	148	TIGHT THERMAL	0.05	0.5
3	1	A	1298	TIGHT POSITIONAL	0.05	0.05
3	2	B	1298	TIGHT POSITIONAL	0.05	0.05
3	3	C	1298	TIGHT POSITIONAL	0.05	0.05
3	4	D	1298	TIGHT POSITIONAL	0.05	0.05
3	5	E	1298	TIGHT POSITIONAL	0.05	0.05
3	1	A	1298	TIGHT THERMAL	0.09	0.5
3	2	B	1298	TIGHT THERMAL	0.08	0.5
3	3	C	1298	TIGHT THERMAL	0.08	0.5
3	4	D	1298	TIGHT THERMAL	0.08	0.5
3	5	E	1298	TIGHT THERMAL	0.08	0.5
4	1	C	42	TIGHT POSITIONAL	0.03	0.05
4	2	A	42	TIGHT POSITIONAL	0.04	0.05
4	3	E	42	TIGHT POSITIONAL	0.03	0.05
4	4	D	42	TIGHT POSITIONAL	0.03	0.05
4	1	C	42	TIGHT THERMAL	0.05	0.5
4	2	A	42	TIGHT THERMAL	0.05	0.5
4	3	E	42	TIGHT THERMAL	0.06	0.5
4	4	D	42	TIGHT THERMAL	0.06	0.5

LS refinement shell

Resolution: 2.882→2.955 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	83	-
R_work	0.256	1953	-
obs	-	2036	83.27 %

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	1.5185	-0.0795	0.2897	2.9221	-0.205	1.8309	-0.0624	0.0106	-0.0688	0.006	0.033	0.0881	0.1263	-0.2116	0.0293	-0.2582	0.0149	0.0301	-0.0903	-0.0331	-0.189	5.1082	29.4505	10.0114
2	1.8893	0.4729	-0.455	1.4551	0.0176	1.7936	-0.0719	0.2314	-0.0402	-0.2045	0.0089	0.0774	-0.0199	-0.1309	0.0629	-0.1608	0.0335	-0.0063	-0.1119	0.0281	-0.1919	19.0118	34.8105	-12.2117
3	2.2438	0.0872	-0.0958	2.2839	0.7525	2.4371	-0.1681	0.2776	-0.1562	-0.0009	0.0794	-0.0226	0.1866	0.122	0.0887	-0.2042	-0.0692	0.0661	-0.0825	0.0414	-0.1349	45.1795	32.5217	-5.7054
4	1.8287	-0.4839	-0.246	3.8451	-0.3777	2.8953	-0.1182	-0.0841	-0.2225	-0.0401	-0.0282	-0.3149	0.2701	0.2907	0.1464	-0.2206	-0.0062	-0.0256	-0.0728	-0.0126	-0.1216	47.0892	26.271	20.1672
5	2.7879	0.2227	0.0469	2.7331	-0.037	1.8654	-0.08	-0.2081	-0.3086	0.0941	0.049	-0.1113	0.1586	-0.0741	0.031	-0.1672	0.0041	0.0388	-0.0878	-0.0139	-0.2602	22.2278	24.3154	29.9345

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-5 - 209
2	X-RAY DIFFRACTION	2	B	-5 - 208
3	X-RAY DIFFRACTION	3	C	-4 - 208
4	X-RAY DIFFRACTION	4	D	-5 - 208
5	X-RAY DIFFRACTION	5	E	-4 - 208

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