PDB-5lxb: Crystal structure of a mutant binding protein (5HTBP-AChBP) in co...

ID or keywords:

Entry

Database: PDB / ID: 5lxb

Title

Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with palonosetron

Components

Soluble acetylcholine receptor

Keywords

acetylcholine binding protein / Cys-loop receptor / 5-HT3 receptor

Function / homology

Function and homology information

excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynapse / neuron projection / identical protein binding / membrane / metal ion binding
Similarity search - Function

Biological species

Aplysia californica (California sea hare)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.34 Å

Authors

Ulens, C.

Funding support

Belgium, 1items

Citation

Journal: ACS Chem Neurosci / Year: 2016
Title: Palonosetron-5-HT3 Receptor Interactions As Shown by a Binding Protein Cocrystal Structure.
Authors: Price, K.L. / Lillestol, R.K. / Ulens, C. / Lummis, S.C.

History

Deposition	Sep 20, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 12, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 11, 2017	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.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	5lxb.cif.gz	830.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5lxb.ent.gz	696.7 KB	Display	PDB format
PDBx/mmJSON format	5lxb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5lxb_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	5lxb_full_validation.pdf.gz	2.7 MB	Display
Data in XML	5lxb_validation.xml.gz	76.5 KB	Display
Data in CIF	5lxb_validation.cif.gz	101.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lx/5lxb ftp://data.pdbj.org/pub/pdb/validation_reports/lx/5lxb	HTTPS FTP

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Related structure data

Related structure data	2ymeS S: Starting model for refinement
Similar structure data	2w8f-1 2yme-2 6qkk-2 6sh0-1 5oal-3 6qqo-2 5oa0-d 2xnu-d 5oaj-2 5oal-2 2y58-d 5oad-d 2xnt-1 2yme-1 2w8f-2 2w8g-d 6sgv-1 5oal-1 5oaj-1 5o8t-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

2ymeS

S: Starting model for refinement

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

279 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 software
140 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 software
139 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.215, 137.051, 131.249
Angle α, β, γ (deg.)	90.000, 93.780, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 205 / Label seq-ID: 20 - 224

NCS ensembles :

#1: Protein

Soluble acetylcholine receptor

Mass: 27526.949 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Aplysia californica (California sea hare)
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.: 8
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-7A9 / palonosetron

Mass: 296.407 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₁₉H₂₄N₂O / Comment: medication, chemotherapy, antagonist*YM

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.78 Å³/Da / Density % sol: 55.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 200 mM sodium 265 citrate, 100 mM bis tris propane pH 8.5, and 20% (w/v) PEG3350.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
Detector	Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Dec 12, 2004
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873 Å / Relative weight: 1
Reflection	Resolution: 2.34→130.96 Å / Num. obs: 106052 / % possible obs: 99.2 % / Redundancy: 4.5 % / Net I/σ(I): 8.9
Reflection shell	Resolution: 2.34→2.47 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.845 / Mean I/σ(I) obs: 1.6 / CC_1/2: 0.598 / % possible all: 94.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0157	refinement
PDB_EXTRACT	3.2	data extraction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2yme

2yme

Resolution: 2.34→130.96 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.934 / SU B: 21.316 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.373 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.245	5294	5 %	RANDOM
R_work	0.2179	-	-	-
obs	0.2192	100742	98.82 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK

Displacement parameters

B_iso max: 163.22 Å² / B_iso mean: 55.902 Å² / B_iso min: 26.88 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.76 Å²	-0 Å²	2.23 Å²
2-	-	0.45 Å²	0 Å²
3-	-	-	0.01 Å²

Refinement step

Cycle: final / Resolution: 2.34→130.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16400	0	266	280	16946
B_iso mean	-	-	73.36	49.8	-
Num. residues	-	-	-	-	2050

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.02	17123
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	15206
X-RAY DIFFRACTION	r_angle_refined_deg	1.819	1.968	23403
X-RAY DIFFRACTION	r_angle_other_deg	1.005	3	35426
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.754	5	2040
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.352	24.304	790
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.042	15	2730
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.999	15	100
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	2630
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	18815
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3497
X-RAY DIFFRACTION	r_mcbond_it	2.921	2.093	8190
X-RAY DIFFRACTION	r_mcbond_other	2.921	2.093	8189
X-RAY DIFFRACTION	r_mcangle_it	4.174	3.142	10220

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	13002	0.06
1	2	B	13002	0.06
2	1	A	12948	0.07
2	2	C	12948	0.07
3	1	A	12926	0.06
3	2	D	12926	0.06
4	1	A	12944	0.06
4	2	E	12944	0.06
5	1	A	12968	0.07
5	2	F	12968	0.07
6	1	A	12898	0.07
6	2	G	12898	0.07
7	1	A	13036	0.06
7	2	H	13036	0.06
8	1	A	13128	0.06
8	2	I	13128	0.06
9	1	A	13054	0.06
9	2	J	13054	0.06
10	1	B	13150	0.05
10	2	C	13150	0.05
11	1	B	13066	0.05
11	2	D	13066	0.05
12	1	B	13030	0.06
12	2	E	13030	0.06
13	1	B	12894	0.07
13	2	F	12894	0.07
14	1	B	13058	0.06
14	2	G	13058	0.06
15	1	B	13084	0.07
15	2	H	13084	0.07
16	1	B	13086	0.06
16	2	I	13086	0.06
17	1	B	13110	0.05
17	2	J	13110	0.05
18	1	C	13188	0.04
18	2	D	13188	0.04
19	1	C	12992	0.07
19	2	E	12992	0.07
20	1	C	12878	0.07
20	2	F	12878	0.07
21	1	C	13040	0.06
21	2	G	13040	0.06
22	1	C	13062	0.06
22	2	H	13062	0.06
23	1	C	13098	0.05
23	2	I	13098	0.05
24	1	C	13098	0.06
24	2	J	13098	0.06
25	1	D	12988	0.07
25	2	E	12988	0.07
26	1	D	12896	0.06
26	2	F	12896	0.06
27	1	D	13006	0.06
27	2	G	13006	0.06
28	1	D	13000	0.07
28	2	H	13000	0.07
29	1	D	13076	0.05
29	2	I	13076	0.05
30	1	D	13046	0.06
30	2	J	13046	0.06
31	1	E	12808	0.08
31	2	F	12808	0.08
32	1	E	12936	0.07
32	2	G	12936	0.07
33	1	E	13026	0.07
33	2	H	13026	0.07
34	1	E	12922	0.07
34	2	I	12922	0.07
35	1	E	12994	0.06
35	2	J	12994	0.06
36	1	F	12940	0.06
36	2	G	12940	0.06
37	1	F	12928	0.07
37	2	H	12928	0.07
38	1	F	13078	0.06
38	2	I	13078	0.06
39	1	F	13004	0.06
39	2	J	13004	0.06
40	1	G	12986	0.08
40	2	H	12986	0.08
41	1	G	12996	0.06
41	2	I	12996	0.06
42	1	G	13088	0.06
42	2	J	13088	0.06
43	1	H	13008	0.07
43	2	I	13008	0.07
44	1	H	13090	0.07
44	2	J	13090	0.07
45	1	I	13094	0.05
45	2	J	13094	0.05

LS refinement shell

Resolution: 2.34→2.401 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.338	360	-
R_work	0.33	6729	-
all	-	7089	-
obs	-	-	89.69 %

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	1.5616	0.5572	-0.0233	1.6158	-0.3703	1.613	-0.061	-0.2166	-0.1327	0.1925	0.0194	-0.0694	-0.0809	0.0502	0.0417	0.3729	0.0401	-0.3412	0.0547	0.0127	0.3714	39.095	12.519	72.637
2	2.0441	0.2395	-0.0365	1.9808	0.0557	1.0941	-0.0277	0.0128	-0.113	0.0924	0.0218	-0.1494	0.0484	0.0519	0.0059	0.3319	0.0047	-0.3342	0.0919	0.068	0.4071	40.888	-14.213	69.895
3	1.8793	-0.267	0.0603	1.0521	-0.2593	2.3625	-0.0696	0.1159	-0.2787	-0.0952	-0.0124	-0.0051	0.2605	0.0844	0.082	0.3464	-0.0226	-0.3306	0.0127	0.0147	0.4536	30.034	-20.915	46.398
4	1.5831	-0.1239	-0.6696	1.8105	0.1572	1.8728	-0.0373	0.2371	-0.0926	-0.0703	0.0887	0.0077	-0.0205	-0.2028	-0.0514	0.3304	-0.021	-0.3796	0.1219	-0.002	0.4632	21.538	1.504	34.491
5	1.7681	0.0717	-0.7615	1.1796	-0.1257	1.9642	0.0145	0.0165	0.0133	0.1058	0.0554	0.0449	-0.1778	-0.1634	-0.0698	0.3534	0.0265	-0.3588	0.0292	0.0083	0.424	27.07	21.9	50.663
6	1.9131	1.0575	-0.9637	1.5299	-0.5884	1.2879	0.1417	-0.3028	0.1916	0.1187	-0.13	-0.0938	-0.1262	0.2421	-0.0116	0.3314	-0.0302	-0.3559	0.1083	-0.0271	0.4707	7.071	41.604	31.24
7	1.5928	0.1186	-0.6791	1.3161	-0.326	1.8881	0.1745	-0.0153	0.426	0.0953	-0.01	0.041	-0.1949	-0.0284	-0.1645	0.3638	-0.0394	-0.2766	0.038	-0.0296	0.5517	2.079	65.406	20.067
8	2.0539	0.0218	0.0375	1.7323	0.3575	1.8737	0.1734	0.1271	0.2387	-0.1767	-0.1146	0.0235	-0.1508	-0.1133	-0.0588	0.395	0.0513	-0.2968	0.0829	0.0898	0.4606	-6.498	61.204	-4.874
9	2.6881	0.0075	-0.4464	2.1075	-0.2459	1.5736	-0.0292	0.0604	-0.1356	-0.2229	-0.0054	0.0449	0.0964	-0.0894	0.0346	0.4223	0.0468	-0.3371	0.1173	0.0195	0.3327	-7.005	34.879	-9.304
10	2.5517	0.1023	-0.4887	1.2638	-0.3683	2.3455	0.0477	0.0491	-0.1148	-0.0948	-0.0839	-0.039	0.1941	-0.0259	0.0362	0.3243	0.0288	-0.3406	0.0116	-0.0259	0.3945	1.44	22.709	13.02

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 205
2	X-RAY DIFFRACTION	2	B	1 - 205
3	X-RAY DIFFRACTION	3	C	1 - 205
4	X-RAY DIFFRACTION	4	D	1 - 205
5	X-RAY DIFFRACTION	5	E	1 - 205
6	X-RAY DIFFRACTION	6	F	1 - 205
7	X-RAY DIFFRACTION	7	G	1 - 205
8	X-RAY DIFFRACTION	8	H	1 - 205
9	X-RAY DIFFRACTION	9	I	1 - 205
10	X-RAY DIFFRACTION	10	J	1 - 205

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