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- PDB-7txf: The allosteric binding mode of alphaD-conotoxin VxXXB -

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Basic information

Entry
Database: PDB / ID: 7txf
TitleThe allosteric binding mode of alphaD-conotoxin VxXXB
Components
  • Acetylcholine-binding protein
  • Alpha-conotoxin VxXXB
KeywordsPEPTIDE BINDING PROTEIN / Alpha-conotoxin / Complex / ACETYLCHOLINE-BINDING PROTEIN / CHOLINE-BINDING PROTEIN-ANTAGONIST 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 / synaptic cleft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / toxin activity / postsynapse / neuron projection ...host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / excitatory extracellular ligand-gated monoatomic ion channel activity / synaptic cleft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / toxin activity / postsynapse / neuron projection / extracellular region / membrane
Similarity search - Function
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 / Ig-like domain profile. / Immunoglobulin-like domain
Similarity search - Domain/homology
Alpha-conotoxin VxXXB / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
Conus vexillum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsHo, T.N.T. / Abraham, N. / Lewis, R.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Front Pharmacol / Year: 2023
Title: Unravelling the allosteric binding mode of alpha D-VxXXB at nicotinic acetylcholine receptors.
Authors: Ho, T.N. / Abraham, N. / Lewis, R.J.
History
DepositionFeb 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Oct 25, 2023Group: Database references / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
F: Alpha-conotoxin VxXXB
G: Alpha-conotoxin VxXXB
H: Alpha-conotoxin VxXXB


Theoretical massNumber of molelcules
Total (without water)126,2448
Polymers126,2448
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.909, 119.573, 150.733
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
Acetylcholine-binding protein / ACh-binding protein / AchBP


Mass: 23262.818 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Production host: Escherichia coli (E. coli) / References: UniProt: P58154
#2: Protein/peptide Alpha-conotoxin VxXXB / Vx20.2 / VxXIIB


Mass: 3309.879 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Conus vexillum (invertebrata) / References: UniProt: P0C1W6
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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 0.91 M lithium chloride, 16% PEG6000 and 0.1 M MES monohydrate pH 6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 2.47→46.36 Å / Num. obs: 45467 / % possible obs: 99.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.5
Reflection shellResolution: 2.47→2.55 Å / Rmerge(I) obs: 1.178 / Num. unique obs: 4181

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLM3.27data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T90

5t90


Resolution: 2.47→46.36 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.93 / SU B: 26.193 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.615 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24635 1876 4.4 %RANDOM
Rwork0.19826 ---
obs0.20033 41036 94.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.488 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-0 Å2
2---0.62 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.47→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8772 0 0 0 8772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0178985
X-RAY DIFFRACTIONr_bond_other_d0.0020.0198176
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.84512255
X-RAY DIFFRACTIONr_angle_other_deg1.1292.64718851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.15251092
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48121.567504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.001151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8971577
X-RAY DIFFRACTIONr_chiral_restr0.1050.21375
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210156
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022110
X-RAY DIFFRACTIONr_mcbond_it2.764.7724401
X-RAY DIFFRACTIONr_mcbond_other2.764.7714399
X-RAY DIFFRACTIONr_mcangle_it4.4287.1555482
X-RAY DIFFRACTIONr_mcangle_other4.4287.1555482
X-RAY DIFFRACTIONr_scbond_it3.2485.1014584
X-RAY DIFFRACTIONr_scbond_other3.2485.1014584
X-RAY DIFFRACTIONr_scangle_other5.097.5146773
X-RAY DIFFRACTIONr_long_range_B_refined7.90755.5219530
X-RAY DIFFRACTIONr_long_range_B_other7.90855.5119528
LS refinement shellResolution: 2.47→2.531 Å
RfactorNum. reflection% reflection
Rfree0.375 113 -
Rwork0.347 2400 -
obs--76.13 %
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)
13.4228-0.62160.24783.9249-1.52032.95430.0449-0.39970.14340.4944-0.1661-0.2386-0.43570.18430.12120.2596-0.0465-0.04310.18650.04260.05438.83218.23633.785
22.1807-0.5676-0.15773.8009-0.08261.24650.17620.2004-0.3248-0.2996-0.1185-0.26740.22550.0869-0.05770.16060.0312-0.00530.12570.01330.139922.3072.638-3.882
32.06330.1124-0.1422.90191.27283.6891-0.1182-0.2494-0.52910.3656-0.00110.24880.36930.0830.11940.2607-0.0249-0.02990.12340.17610.3361.426-7.88832.479
42.59630.3495-0.22962.2096-0.36633.2856-0.0950.0321-0.5957-0.0395-0.03470.06320.38210.10940.12980.28280.0179-0.04060.1130.02790.380310.045-17.2038.787
52.4348-0.345-0.68311.12430.41021.1829-0.0037-0.0998-0.0167-0.0092-0.0391-0.2374-0.1550.1650.04280.1324-0.0331-0.02750.08820.06460.087421.70124.3111.377
66.718-0.5061-3.062412.836-1.68153.97740.0425-0.14170.4289-0.38730.26510.1889-0.235-0.0322-0.30760.36760.0438-0.08690.24590.06910.2782-0.9075.78854.242
73.4433-0.9369-0.27599.51685.8866.2372-0.22810.2146-1.9434-0.09360.1169-0.27411.0428-0.25290.11120.84210.02490.18660.6681-0.10961.385422.555-21.711-11.898
86.13551.5738-4.75351.8307-0.325812.0891-0.5056-0.1949-0.3829-0.2275-0.399-0.17420.8967-0.33640.90470.5304-0.0239-0.03260.49890.09060.69942.138-31.21527.315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 205
2X-RAY DIFFRACTION2B1 - 205
3X-RAY DIFFRACTION3C1 - 205
4X-RAY DIFFRACTION4D1 - 204
5X-RAY DIFFRACTION5E1 - 205
6X-RAY DIFFRACTION6F1 - 30
7X-RAY DIFFRACTION7G1 - 30
8X-RAY DIFFRACTION8H1 - 30

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