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- PDB-5t90: Structural mechanisms for alpha-conotoxin selectivity at the huma... -

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Basic information

Entry
Database: PDB / ID: 5t90
TitleStructural mechanisms for alpha-conotoxin selectivity at the human alpha3beta4 nicotinic acetylcholine receptor
Components
  • Acetylcholine-binding protein
  • LsIA
KeywordsPROTEIN BINDING / alpha-conotoxins / acetylcholine binding protein / nicotinic acetylcholine receptor
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic cleft / response to nicotine / neuron projection / synapse / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Mainly Beta
Similarity search - Domain/homology
Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
Conus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAbraham, N. / Healy, M. / Ragnarsson, L. / Brust, A. / Alewood, P. / Lewis, R.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1072113 Australia
CitationJournal: Sci Rep / Year: 2017
Title: Structural mechanisms for alpha-conotoxin activity at the human alpha 3 beta 4 nicotinic acetylcholine receptor.
Authors: Abraham, N. / Healy, M. / Ragnarsson, L. / Brust, A. / Alewood, P.F. / Lewis, R.J.
History
DepositionSep 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

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: LsIA
G: LsIA
H: LsIA
I: LsIA
J: LsIA


Theoretical massNumber of molelcules
Total (without water)128,06810
Polymers128,06810
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20990 Å2
ΔGint-87 kcal/mol
Surface area43680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.940, 124.500, 154.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Acetylcholine-binding protein / AchBP


Mass: 23862.523 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
LsIA


Mass: 1751.003 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Conus (invertebrata)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 0.871 M ammonium sulphate, 7.55% PEG 3350, 2-propanol 7.45% and ammonium acetate 0.1 M pH 4.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→51.4 Å / Num. obs: 26929 / % possible obs: 96.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 62.31 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZDH

3zdh


Resolution: 2.8→48.44 Å / Cor.coef. Fo:Fc: 0.8737 / Cor.coef. Fo:Fc free: 0.8691 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.386
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1354 5.03 %RANDOM
Rwork0.2176 ---
obs0.219 26898 96.69 %-
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1--36.1287 Å20 Å20 Å2
2--12.4273 Å20 Å2
3---23.7014 Å2
Refine analyzeLuzzati coordinate error obs: 0.473 Å
Refinement stepCycle: 1 / Resolution: 2.8→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8622 0 0 85 8707
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0078823HARMONIC2
X-RAY DIFFRACTIONt_angle_deg112036HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3002SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes250HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1246HARMONIC5
X-RAY DIFFRACTIONt_it8823HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.75
X-RAY DIFFRACTIONt_other_torsion18.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1191SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9441SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.91 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2959 143 5.13 %
Rwork0.2523 2645 -
all0.2546 2788 -
obs--96.69 %
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)
11.3614-0.239-0.02762.3864-0.33593.03560.14290.0244-0.01170.4685-0.1385-0.0176-0.05710.0777-0.0043-0.0222-0.0485-0.0691-0.1225-0.0388-0.1534-7.5692-15.2289-7.1687
21.38830.10221.19631.28750.25463.36880.05440.0581-0.43920.1155-0.21590.35970.5699-0.35020.16150.039-0.22360.0925-0.2406-0.0286-0.0466-22.907-52.9809-23.379
32.31931.78380.67392.5015-0.20152.2537-0.04390.11570.3874-0.01020.11890.5405-0.385-0.4164-0.075-0.18970.09770.0014-0.03250.0304-0.0725-26.0465-9.1938-26.1541
42.1032-0.08150.0633.1728-1.04792.1132-0.03530.4282-0.0022-0.02860.03420.5498-0.104-0.40880.0011-0.3234-0.1911-0.09530.1678-0.0166-0.1262-35.2988-32.6955-36.3215
51.3015-0.0893-0.05193.89180.37072.27060.0677-0.2112-0.23740.4779-0.1158-0.04390.56640.03670.04820.05840.0063-0.0303-0.20370.0773-0.2035-5.8379-42.3288-5.297
60.1196-0.47040.06930.07381.84510.67490.0003-0.0614-0.02550.0482-0.0241-0.0672-0.00660.04870.02380.1107-0.03420.0807-0.0448-0.0613-0.0073-9.0598-0.55-12.0381
70-0.32390.35080.9709-1.62620.58080.00750.0138-0.04830.0083-0.00910.07970.0157-0.03260.00160.2284-0.0478-0.0133-0.15650.1725-0.0226-12.9123-62.3829-15.7787
80-0.5330.67490.01220.1470.5539-0.0097-0.0385-0.09520.00380.0037-0.030.03370.04030.0060.11960.0454-0.15680.04820.0917-0.10564.2214-33.51911.7458
900.4752-0.27060.05290.28550.31080.00320.01820.0034-0.0147-0.00580.0272-0.016-0.04240.00270.0088-0.1094-0.03260.0543-0.0878-0.0012-36.8854-46.8564-40.0544
100.10240.62080.20620.0499-0.26130-0.0012-0.00740.02160.01260.00230.0418-0.0363-0.0079-0.00120.01010.0173-0.14880.03870.14740.0405-35.444-10.0981-38.2945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }

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