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- PDB-5xgl: Co-crystal structure of Ac-AChBPP in complex with alpha-conotoxin LvIA -

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Basic information

Entry
Database: PDB / ID: 5xgl
TitleCo-crystal structure of Ac-AChBPP in complex with alpha-conotoxin LvIA
Components
  • Alpha-conotoxin LvIA
  • Soluble acetylcholine receptor
KeywordsMETAL BINDING PROTEIN/TOXIN / Co-crystal structure / alpha-conotoxin / Ac-AChBP / METAL BINDING PROTEIN-TOXIN complex
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / 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 / toxin activity / postsynapse / neuron projection / extracellular region ...host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / 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 / toxin activity / postsynapse / neuron projection / extracellular region / identical protein binding / membrane / metal ion binding
Similarity search - Function
Conotoxin, alpha-type / Alpha conotoxin precursor / Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / 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 ...Conotoxin, alpha-type / Alpha conotoxin precursor / Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / 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
Alpha-conotoxin LvIA / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
Conus lividus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.439 Å
AuthorsWang, X.Q. / Xu, M.Y. / Luo, S.L. / Zhu, X.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470751, 81420108028 and U1405228 China
CitationJournal: Protein Cell / Year: 2017
Title: The crystal structure of Ac-AChBP in complex with alpha-conotoxin LvIA reveals the mechanism of its selectivity towards different nAChR subtypes
Authors: Xu, M. / Zhu, X. / Yu, J. / Yu, J. / Luo, S. / Wang, X.
History
DepositionApr 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble acetylcholine receptor
F: Alpha-conotoxin LvIA
B: Soluble acetylcholine receptor
C: Alpha-conotoxin LvIA
D: Soluble acetylcholine receptor
E: Alpha-conotoxin LvIA
G: Soluble acetylcholine receptor
H: Alpha-conotoxin LvIA
I: Soluble acetylcholine receptor
J: Alpha-conotoxin LvIA


Theoretical massNumber of molelcules
Total (without water)136,44710
Polymers136,44710
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21050 Å2
ΔGint-121 kcal/mol
Surface area43070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.389, 83.991, 209.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Soluble acetylcholine receptor


Mass: 25604.537 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): SF9 / Production host: Baculovirus expression vector pCTdual / References: UniProt: Q8WSF8
#2: Protein/peptide
Alpha-conotoxin LvIA / Alpha-CTx LvIA


Mass: 1684.918 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Conus lividus (invertebrata) / References: UniProt: L8BU87

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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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Bis-Tris propane PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.4→28.438 Å / Num. obs: 18406 / % possible obs: 98 % / Redundancy: 5 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.5
Reflection shellResolution: 3.44→3.56 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CO5

5co5


Resolution: 3.439→28.438 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2826 906 4.92 %
Rwork0.2391 --
obs0.2412 18406 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.439→28.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8835 0 0 0 8835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049067
X-RAY DIFFRACTIONf_angle_d0.6612381
X-RAY DIFFRACTIONf_dihedral_angle_d14.8015495
X-RAY DIFFRACTIONf_chiral_restr0.0461380
X-RAY DIFFRACTIONf_plane_restr0.0051605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4393-3.65440.30591390.29632547X-RAY DIFFRACTION87
3.6544-3.93590.3761350.29352947X-RAY DIFFRACTION100
3.9359-4.33070.27111560.25462924X-RAY DIFFRACTION100
4.3307-4.95450.29811560.22342969X-RAY DIFFRACTION100
4.9545-6.23140.25261570.22462981X-RAY DIFFRACTION100
6.2314-28.4390.26141630.21763132X-RAY DIFFRACTION100

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