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- PDB-2byq: Crystal structure of Aplysia californica AChBP in complex with ep... -

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Basic information

Entry
Database: PDB / ID: 2byq
TitleCrystal structure of Aplysia californica AChBP in complex with epibatidine
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / ACETYLCHOLINE BINDING PROTEIN / NICOTINIC ACETYLCHOLINE / CONFORMATIONAL FLEXIBILITY / AGONIST
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / 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
EPIBATIDINE / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHansen, S.B. / Sulzenbacher, G. / Huxford, T. / Marchot, P. / Taylor, P. / Bourne, Y.
CitationJournal: Embo J. / Year: 2005
Title: Structures of Aplysia Achbp Complexes with Nicotinic Agonists and Antagonists Reveal Distinctive Binding Interfaces and Conformations.
Authors: Hansen, S.B. / Sulzenbacher, G. / Huxford, T. / Marchot, P. / Taylor, P. / Bourne, Y.
History
DepositionAug 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,30710
Polymers129,2645
Non-polymers1,0435
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)200.925, 200.925, 200.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23A

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPPHEPHEAA-3 - 145 - 22
211ASPASPPHEPHEBB-3 - 145 - 22
121TYRTYRTRPTRPAA20 - 6728 - 75
221TYRTYRTRPTRPBB20 - 6728 - 75
131ILEILEGLUGLUAA75 - 20683 - 214
231ILEILEGLUGLUBB75 - 20683 - 214
112ASPASPPHEPHECC-3 - 145 - 22
212ASPASPPHEPHEDD-3 - 145 - 22
122TYRTYRTRPTRPCC20 - 6728 - 75
222TYRTYRTRPTRPDD20 - 6728 - 75
132ILEILEGLUGLUCC75 - 20683 - 214
232ILEILEGLUGLUDD75 - 20683 - 214
113ASPASPPHEPHEEE-3 - 145 - 22
213ASPASPPHEPHEAA-3 - 145 - 22
123TYRTYRTRPTRPEE20 - 6728 - 75
223TYRTYRTRPTRPAA20 - 6728 - 75
133ILEILEGLUGLUEE75 - 20683 - 214
233ILEILEGLUGLUAA75 - 20683 - 214

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR


Mass: 25852.744 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Cell: SENSORY CELL / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-EPJ / EPIBATIDINE / (2R)-2-(6-CHLOROPYRIDIN-3-YL)-7-AZABICYCLO[2.2.1]HEPTANE / Epibatidine


Mass: 208.687 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H13ClN2 / Comment: alkaloid*YM

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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: 2.81 Å3/Da / Density % sol: 55.92 %
Crystal growpH: 7.5
Details: 18-22% PEG-3350, 0.1 M TRIS, PH 7.5, 0.2 M SODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 18257 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BYN

2byn


Resolution: 3.4→30 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.828 / SU B: 62.72 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.631 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 929 5.1 %RANDOM
Rwork0.18 ---
obs0.184 17132 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.41 Å2
Refinement stepCycle: LAST / Resolution: 3.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8515 0 70 0 8585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228813
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9612020
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47251063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15924.524420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.471151425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.451550
X-RAY DIFFRACTIONr_chiral_restr0.1040.21339
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026744
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.24103
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.25955
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2315
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2711.55468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.48228743
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.77233841
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2924.53277
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A789tight positional0.060.05
2C783tight positional0.070.05
3E789tight positional0.050.05
1A766medium positional0.430.5
2C771medium positional0.490.5
3E770medium positional0.450.5
1A789tight thermal0.060.5
2C783tight thermal0.060.5
3E789tight thermal0.060.5
1A766medium thermal0.362
2C771medium thermal0.422
3E770medium thermal0.42
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 68
Rwork0.249 1259
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)
12.68080.86760.12431.64630.04543.0022-0.00580.1524-0.2979-0.24310.04090.18580.2386-0.3439-0.0351-0.18440.0886-0.0027-0.10330.1038-0.112951.459445.1179-0.7151
22.2253-0.1681-0.10243.4803-0.14261.6267-0.07750.0723-0.3029-0.10720.16240.37550.3534-0.1982-0.0849-0.20250.06890.0677-0.07650.1285-0.184448.503232.533922.3068
31.8235-0.3741-0.61462.9193-0.13971.3579-0.15220.0624-0.31710.1160.0567-0.03930.27970.05790.0954-0.23030.07080.0186-0.10790.0276-0.204172.369425.292931.4352
41.8323-0.5472-0.44692.3373-0.33362.9754-0.02610.1568-0.1838-0.0402-0.03820.04280.16920.07270.0643-0.33920.01790.035-0.14940.0591-0.225189.729832.489113.3476
53.22390.2880.48892.11491.07153.36820.04820.2785-0.2535-0.31910.06280.1160.0841-0.1011-0.111-0.18730.01340.0162-0.20660.0859-0.26777.225844.9348-6.2954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 208
2X-RAY DIFFRACTION2B-5 - 208
3X-RAY DIFFRACTION3C-6 - 208
4X-RAY DIFFRACTION4D-5 - 208
5X-RAY DIFFRACTION5E-4 - 208

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