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- PDB-4frr: X-ray structure of Acetylcholine binding protein from Aplysia cal... -

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Basic information

Entry
Database: PDB / ID: 4frr
TitleX-ray structure of Acetylcholine binding protein from Aplysia californica in presence of 3-((S)-azetidin-2-ylmethoxy)-5-((1S,2R)-2-(2-methoxyethyl)cyclopropyl)pyridine
ComponentsSoluble acetylcholine receptor
KeywordsACETYLCHOLINE BINDING PROTEIN / nactivates released acetylcholine at cholinergic synapses / Homopentameric Acetycholine Binding Protein
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / identical protein binding / membrane / metal ion binding
Similarity search - Function
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-0VC / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMukhopadhyay, S. / Mesecar, A.D.
CitationJournal: To be Published
Title: X-ray structure of Acetylcholine binding protein from Aplysia californica in presence of 3-((S)-azetidin-2-ylmethoxy)-5-((1S,2R)-2-(2-methoxyethyl)cyclopropyl)pyridine
Authors: Mukhopadhyay, S. / Mesecar, A.D.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 2023Group: 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)265,19142
Polymers261,22310
Non-polymers3,96932
Water14,808822
1
A: Soluble acetylcholine receptor
B: Soluble acetylcholine receptor
C: Soluble acetylcholine receptor
D: Soluble acetylcholine receptor
E: Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,78023
Polymers130,6115
Non-polymers2,16818
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-65 kcal/mol
Surface area45470 Å2
MethodPISA
2
F: Soluble acetylcholine receptor
G: Soluble acetylcholine receptor
H: Soluble acetylcholine receptor
I: Soluble acetylcholine receptor
J: Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,41119
Polymers130,6115
Non-polymers1,80014
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12660 Å2
ΔGint-60 kcal/mol
Surface area45890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.270, 139.735, 146.399
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Soluble acetylcholine receptor


Mass: 26122.256 Da / Num. of mol.: 10 / Fragment: UNP residues 18-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Plasmid: pFLAG-CMV-3 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-0VC / 3-[(2S)-azetidin-2-ylmethoxy]-5-[(1S,2R)-2-(2-methoxyethyl)cyclopropyl]pyridine


Mass: 262.347 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H22N2O2
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris HCl,7.5, 15% PEG 4000 and 0.2M MgCl2 . , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→200 Å / Num. obs: 142663 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.096 / Χ2: 1.103 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.246.70.84969530.827198.7
2.24-2.286.90.78870340.826199.4
2.28-2.3270.68270940.835199.8
2.32-2.377.10.60370340.846199.7
2.37-2.427.10.51870620.868199.9
2.42-2.487.10.46870700.875199.9
2.48-2.547.20.41870790.891199.9
2.54-2.617.20.34970870.901199.9
2.61-2.697.20.28671250.9211100
2.69-2.777.30.24270690.965199.9
2.77-2.877.30.20171051.0731100
2.87-2.997.30.16371311.1821100
2.99-3.127.40.13471301.2331100
3.12-3.297.40.09771061.1841100
3.29-3.497.50.07671841.1861100
3.49-3.767.60.06671461.3381100
3.76-4.147.50.06472021.9611100
4.14-4.747.50.04672161.6651100
4.74-5.977.50.03773121.1871100
5.97-2007.10.03175241.101199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WN9

2wn9


Resolution: 2.2→101.08 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 11.434 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 7147 5 %RANDOM
Rwork0.1972 ---
obs0.1997 142574 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.76 Å2 / Biso mean: 42.362 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2--3.2 Å20 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→101.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16773 0 270 822 17865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217803
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.96424262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93952144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01424.281848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.646152861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8115110
X-RAY DIFFRACTIONr_chiral_restr0.1050.22694
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113608
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 452 -
Rwork0.274 9401 -
all-9853 -
obs--98.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
115.4964-0.9383.743815.25290.937519.52640.3569-1.0522-1.32780.46030.08680.23790.6299-0.6978-0.44370.3286-0.10280.02650.1585-0.00210.4568100.46675.299-11.8343
21.82850.22490.13141.24930.34071.4856-0.00030.1883-0.0642-0.13960.0352-0.03190.04420.096-0.03480.028-0.00220.00470.08940.01110.0123116.189330.5483-8.9443
317.8865-0.3219-6.415212.82791.537416.7009-0.2895-0.8806-0.12450.4075-0.06890.08790.26790.01930.35850.3116-0.1248-0.14070.11260.05250.205577.59818.29023.6425
41.55720.48640.00591.3461-0.07491.1724-0.00750.16980.0031-0.1302-0.00240.0088-0.0359-0.11420.010.04590.0239-0.02220.11090.0130.022788.797133.2607-10.5097
520.6567-3.03112.353716.6259-1.81013.44070.6919-0.0962-1.26870.0097-0.0136-0.44161.25760.7104-0.67820.68630.1767-0.21660.32880.0130.512484.39158.125328.7819
61.51110.0370.13591.1031-0.15081.50640.0194-0.16910.0080.05180.00220.17770.0419-0.2298-0.02160.04290.0287-0.00820.1186-0.01110.061878.896435.414815.2529
715.429-0.7212-5.3014.75092.10573.9359-0.38321.3794-1.4731-0.332-0.13790.32160.1473-0.24450.5210.76190.1424-0.02680.41910.01090.5669109.11434.801728.1398
81.8238-0.0667-0.25541.9078-0.28091.69850.0182-0.2702-0.02260.140.01280.03470.01210.0103-0.0310.04960.0023-0.01320.1663-0.01740.0101100.089433.47332.8642
97.3672-0.7692-0.64287.3595-0.683226.5671-0.0270.503-0.0934-0.30630.23960.16261.3408-1.2449-0.21270.41060.0068-0.05460.1989-0.05980.5765120.74263.31341.8977
101.2413-0.1108-0.14971.1851-0.08021.6633-0.0273-0.1593-0.04690.1138-0.0039-0.17830.05090.24790.03120.0194-0.0071-0.02260.15650.01040.0589122.985230.444917.6194
1113.4853-1.5458-6.25228.0962.35673.8203-0.3316-2.0642-2.0144-0.09380.03080.00340.3590.10650.30090.5558-0.3073-0.19091.58520.84451.0508123.689874.5958-11.9993
121.7086-0.14280.11751.482-0.03451.67370.06970.2092-0.0335-0.1813-0.0235-0.03620.02990.1362-0.04610.0730.00960.00370.12690.01980.0118138.683100.4067-8.9817
131.88550.048-0.34841.8386-0.18492.12220.0798-0.046-0.50560.1655-0.05350.17290.501-0.4675-0.02630.2449-0.0299-0.0550.30590.03970.1833108.041293.2407-5.7333
141.85320.1825-0.09681.4333-0.02982.24910.03150.1653-0.013-0.10820.02280.06510.063-0.2615-0.05420.08370.0468-0.03530.16450.02920.0385110.9082103.1094-10.7809
1519.8595-2.1311-2.309513.1651-0.24810.42360.07840.3052-0.9421-0.24820.1677-0.32340.25590.0055-0.24610.77430.0553-0.3430.2072-0.04580.7749106.761876.785427.7287
161.3748-0.06460.17411.266-0.26571.57020.0238-0.08670.03270.08020.05010.2248-0.0122-0.3026-0.07380.10110.0364-0.00040.19620.00430.0757101.1771104.463115.2657
1719.4026-1.2232-2.492910.09622.03017.8071-0.01221.1183-1.3891-0.0829-0.33540.41510.5321-0.20710.34770.6120.06730.04170.2974-0.01730.3959131.86274.413827.9441
181.7899-0.2063-0.24271.7672-0.14491.73060.0515-0.2174-0.01120.1269-0.0150.0486-0.05380.0118-0.03660.0846-0.0283-0.01540.142-0.01710.012122.3893102.646632.8136
197.8513-0.46731.529710.78933.21619.13040.23160.32810.14140.04360.00710.19190.6756-1.0498-0.23870.23140.0492-0.0790.11470.01020.3731143.84273.37252.4424
201.1105-0.3291-0.22021.33230.16231.61530.0131-0.14930.0370.1103-0.0156-0.1881-0.09350.3180.00250.0528-0.046-0.01610.17440.00970.0631145.5165100.546917.5591
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 18
2X-RAY DIFFRACTION2A20 - 208
3X-RAY DIFFRACTION3B-3 - 18
4X-RAY DIFFRACTION4B20 - 208
5X-RAY DIFFRACTION5C-2 - 18
6X-RAY DIFFRACTION6C20 - 208
7X-RAY DIFFRACTION7D-2 - 19
8X-RAY DIFFRACTION8D20 - 208
9X-RAY DIFFRACTION9E-4 - 17
10X-RAY DIFFRACTION10E20 - 208
11X-RAY DIFFRACTION11F-1 - 19
12X-RAY DIFFRACTION12F20 - 208
13X-RAY DIFFRACTION13G-3 - 66
14X-RAY DIFFRACTION14G67 - 208
15X-RAY DIFFRACTION15H-1 - 18
16X-RAY DIFFRACTION16H20 - 208
17X-RAY DIFFRACTION17I-2 - 19
18X-RAY DIFFRACTION18I20 - 207
19X-RAY DIFFRACTION19J-5 - 19
20X-RAY DIFFRACTION20J20 - 208

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