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- PDB-4bqt: Aplysia californica AChBP in complex with Cytisine -

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Basic information

Entry
Database: PDB / ID: 4bqt
TitleAplysia californica AChBP in complex with Cytisine
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR
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
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-C5E / : / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsRucktooa, P. / Haseler, C.A. / vanElke, R. / Smit, A.B. / Gallagher, T. / Sixma, T.K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Characterization of Binding Mode of Smoking Cessation Drugs to Nicotinic Acetylcholine Receptors Through Study of Ligand Complexes with Acetylcholine-Binding Protein.
Authors: Rucktooa, P. / Haseler, C.A. / Van Elk, R. / Smit, A.B. / Gallagher, T. / Sixma, T.K.
History
DepositionJun 2, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionJun 12, 2013ID: 4AFO
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 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 1.2Dec 20, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)124,84322
Polymers123,4435
Non-polymers1,40017
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14690 Å2
ΔGint-136.3 kcal/mol
Surface area42480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.689, 206.689, 206.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / ACETYLCHOLINE BINDING PROTEIN / ACHBP


Mass: 24688.578 Da / Num. of mol.: 5 / Fragment: RESIDUES 20-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Plasmid: PFASTBAC / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-C5E / (1R,5S)-1,2,3,4,5,6-HEXAHYDRO-8H-1,5-METHANOPYRIDO[1,2-A][1,5]DIAZOCIN-8-ONE / CYTISINE


Mass: 190.242 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H14N2O
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.16 Å3/Da / Density % sol: 61.1 % / Description: NONE
Crystal growpH: 7 / Details: 0.6-1.2 M AMMONIUM SULPHATE, 0.1 M MMT PH 6.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2009 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.88→146.15 Å / Num. obs: 33178 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10
Reflection shellResolution: 2.88→3.04 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.7 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BR7

2br7


Resolution: 2.88→48.72 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / SU B: 30.803 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22415 1667 5.1 %RANDOM
Rwork0.18519 ---
obs0.18711 31312 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.999 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.88→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8213 0 82 25 8320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.028503
X-RAY DIFFRACTIONr_bond_other_d0.0070.027759
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.96211612
X-RAY DIFFRACTIONr_angle_other_deg1.2173.00217894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95951023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58624.447398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.981151369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1391548
X-RAY DIFFRACTIONr_chiral_restr0.0790.21298
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219581
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021935
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2423.6374117
X-RAY DIFFRACTIONr_mcbond_other2.2413.6364114
X-RAY DIFFRACTIONr_mcangle_it3.565.4535130
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5123.8644386
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 2.883→2.958 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 115 -
Rwork0.312 2179 -
obs--94.44 %
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)
12.6543-0.44170.25481.94870.31131.1987-0.0684-0.36220.06040.2530.12010.21430.0372-0.0301-0.05170.08370.04720.04780.24590.0120.045215.322-35.74892.314
21.15010.2589-0.24580.65730.11621.88750.0242-0.09210.1728-0.0520.0416-0.0313-0.1870.0813-0.06590.04280.00820.02380.1343-0.05870.065732.851-28.41673.862
31.43270.12230.2472.7952-0.33421.2791-0.09170.17180.1354-0.18470.08280.0836-0.08690.03250.00890.1084-0.02410.02320.1112-0.01380.039323.576-36.49350.185
41.83370.0468-0.23281.2599-0.61321.5637-0.02490.16190.0083-0.26780.1540.33920.0886-0.1791-0.12910.1538-0.0674-0.07930.06970.00750.1560.269-48.77354.023
51.15750.35530.01350.52550.03882.3532-0.0185-0.15220.00050.01190.06750.2385-0.0222-0.2509-0.04890.0477-0.03230.02580.120.05880.221-4.921-48.24380.042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 321
2X-RAY DIFFRACTION2B1 - 323
3X-RAY DIFFRACTION3C1 - 322
4X-RAY DIFFRACTION4D1 - 323
5X-RAY DIFFRACTION5E1 - 322

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