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- PDB-4bfq: Assembly of a triple pi-stack of ligands in the binding site of A... -

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Basic information

Entry
Database: PDB / ID: 4bfq
TitleAssembly of a triple pi-stack of ligands in the binding site of Aplysia californica acetylcholine binding protein (AChBP)
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / ACETYLCHOLINE BINDING PROTEIN / NICOTINIC ACETYLCHOLINE RECEPTOR / CYS-LOOP RECEPTOR / NACHR / ION CHANNEL / PI-STACKING / TRIPLE LIGAND BINDING / DRUG DESIGN
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-083 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsStornaiuolo, M. / De Kloe, G.E. / Rucktooa, P. / Fish, A. / van Elk, R. / Edink, E.S. / Bertrand, D. / Smit, A.B. / de Esch, I.J.P. / Sixma, T.K.
CitationJournal: Nat.Commun. / Year: 2013
Title: Assembly of a Pi-Pi Stack of Ligands in the Binding Site of an Acetylcholine Binding Protein
Authors: Stornaiuolo, M. / De Kloe, G.E. / Rucktooa, P. / Fish, A. / van Elk, R. / Edink, E.S. / Bertrand, D. / Smit, A.B. / de Esch, I.J.P. / Sixma, T.K.
History
DepositionMar 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Dec 20, 2017Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 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 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)128,49720
Polymers123,4435
Non-polymers5,05415
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14690 Å2
ΔGint-74 kcal/mol
Surface area42960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.730, 78.330, 106.530
Angle α, β, γ (deg.)90.00, 102.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / ACETYLCHOLINE BINDING PROTEIN


Mass: 24688.578 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Cell: GLIAL CELL / Plasmid: PFASTBACI / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-083 / 4,6-dimethyl-N'-(3-pyridin-2-ylisoquinolin-1-yl)pyrimidine-2-carboximidamide


Mass: 354.408 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C21H18N6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSIGNAL SEQUENCE HAS BEEN REMOVED.

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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: 2.86 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8
Details: THE VUF9432-AC-ACHBP COMPLEX WAS FORMED BY MIXING THE PROTEIN AT 3.5 MG/ML WITH 1MM VUF9432 AND INCUBATING ON ICE FOR 1 HOUR. CRYSTALS WERE GROWN USING THE VAPOUR DIFFUSION METHOD IN A ...Details: THE VUF9432-AC-ACHBP COMPLEX WAS FORMED BY MIXING THE PROTEIN AT 3.5 MG/ML WITH 1MM VUF9432 AND INCUBATING ON ICE FOR 1 HOUR. CRYSTALS WERE GROWN USING THE VAPOUR DIFFUSION METHOD IN A SOLUTION CONSISTING OF 0.2M LISO4, 0.8M AMMONIUM SULPHATE IN MMT BUFFER (PH 8.0) AND 19 DEGREES C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9786
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→43.3 Å / Num. obs: 47324 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.8 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0005refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W8E

2w8e
PDB Unreleased entry


Resolution: 2.4→41.26 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 16.766 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.488 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24724 2422 5.1 %RANDOM
Rwork0.20964 ---
obs0.21156 44879 92.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.833 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-0.93 Å2
2---0.61 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8180 0 384 129 8693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.028824
X-RAY DIFFRACTIONr_bond_other_d0.0050.025746
X-RAY DIFFRACTIONr_angle_refined_deg1.3152.00312061
X-RAY DIFFRACTIONr_angle_other_deg1.2163.00313913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29251022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91724.52396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.484151363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0531546
X-RAY DIFFRACTIONr_chiral_restr0.0740.21287
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219779
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021845
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 159 -
Rwork0.33 3199 -
obs--92.25 %
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)
11.10610.12940.33071.349-0.19392.1005-0.0803-0.12890.10420.0642-0.00950.0016-0.27740.09360.08980.07010.01940.02360.1055-0.02750.116819.51413.56229.665
22.04590.077-0.0622.523-0.29391.606-0.0401-0.0846-0.01420.1673-0.0562-0.3005-0.05650.13050.09630.1152-0.0254-0.02870.15120.0020.093831.677-6.18442.997
31.4036-0.0836-0.0641.1689-0.16681.8580.0070.0721-0.0399-0.14120.04580.01320.25740.0464-0.05280.0592-0.02480.01990.1209-0.0060.147913.611-23.7487.561
42.04940.240.17091.32330.30332.49410.09510.1077-0.11730.04240.0346-0.19940.31750.2042-0.12970.13870.0246-0.02240.11450.03130.1627.809-29.46929.753
51.29980.01790.04091.95230.56071.7049-0.0123-0.03770.0553-0.2122-0.0195-0.0227-0.1181-0.02120.03190.02660.0080.01430.13930.02090.15328.4092.7557.408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 303
2X-RAY DIFFRACTION2B1 - 302
3X-RAY DIFFRACTION3D1 - 303
4X-RAY DIFFRACTION4C1 - 303
5X-RAY DIFFRACTION5E1 - 303

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