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- PDB-7n43: Alpha-conotoxin OmIA with unusual pharmacological properties at a... -

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Basic information

Entry
Database: PDB / ID: 7n43
TitleAlpha-conotoxin OmIA with unusual pharmacological properties at alpha7 nicotinic receptors
Components
  • Acetylcholine-binding protein
  • Alpha-conotoxin OmIA
KeywordsCHOLINE-BINDING PROTEIN / Alpha-conotoxin / Acetylcholine-binding protein
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / synaptic cleft / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / toxin activity / synapse / extracellular region / membrane
Similarity search - Function
Conotoxin, alpha-type / Alpha conotoxin precursor / Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / 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 OmIA / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
Conus omaria (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: 2021
Title: Unique Pharmacological Properties of alpha-Conotoxin OmIA at alpha 7 nAChRs.
Authors: Ho, T.N.T. / Abraham, N. / Lewis, R.J.
History
DepositionJun 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
F: Alpha-conotoxin OmIA
G: Alpha-conotoxin OmIA
H: Alpha-conotoxin OmIA
I: Alpha-conotoxin OmIA
J: Alpha-conotoxin OmIA


Theoretical massNumber of molelcules
Total (without water)127,94210
Polymers127,94210
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21300 Å2
ΔGint-99 kcal/mol
Surface area41890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.363, 169.363, 124.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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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
Alpha-conotoxin OmIA


Mass: 1725.974 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Conus omaria (invertebrata) / References: UniProt: P0C1R7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.49 Å3/Da / Density % sol: 64.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 5% PEG4000 and 0.1M sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.47→49.24 Å / Num. obs: 65087 / % possible obs: 99.6 % / Redundancy: 26.85 % / Rsym value: 0.115 / Net I/σ(I): 17.9
Reflection shellResolution: 2.47→2.53 Å / Num. unique obs: 4285 / Rsym value: 1.153

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T90

5t90


Resolution: 2.47→49.19 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 14.552 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21242 2000 3.1 %RANDOM
Rwork0.18668 ---
obs0.18748 63054 99.58 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.052 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å2-0 Å2
2--0.07 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.47→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8717 0 5 146 8868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0178934
X-RAY DIFFRACTIONr_bond_other_d0.0010.0198127
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.84212192
X-RAY DIFFRACTIONr_angle_other_deg1.1022.66718735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35151091
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75922.378492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.839151439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6721565
X-RAY DIFFRACTIONr_chiral_restr0.0960.21383
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022049
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_it3.5642.8534408
X-RAY DIFFRACTIONr_mcbond_other3.5332.8524405
X-RAY DIFFRACTIONr_mcangle_it5.1544.2635481
X-RAY DIFFRACTIONr_mcangle_other5.1554.2635481
X-RAY DIFFRACTIONr_scbond_it4.7563.3114526
X-RAY DIFFRACTIONr_scbond_other4.7563.3114527
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8544.7696712
X-RAY DIFFRACTIONr_long_range_B_refined9.35834.3539672
X-RAY DIFFRACTIONr_long_range_B_other9.36334.3189664
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.47→2.533 Å
RfactorNum. reflection% reflection
Rfree0.304 138 -
Rwork0.302 4369 -
obs--94.57 %
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)
11.65980.0927-0.37991.64450.24091.84270.0688-0.21910.17560.1458-0.0754-0.1316-0.18020.16820.00660.3689-0.0824-0.05370.3451-0.02150.039528.869-33.85745.858
22.3354-0.2281-0.06452.11070.27242.83460.03020.1695-0.0783-0.1219-0.02280.01570.0304-0.2188-0.00730.1977-0.05990.00740.2766-0.04290.0875-7.77-48.95927.679
31.6234-0.15320.08662.97510.59112.0419-0.04550.01250.15590.04450.0294-0.2204-0.29170.24390.01620.2431-0.08490.00450.24950.03350.037733.35-36.06819.287
43.02220.06630.43031.0198-0.02431.67680.0088-0.46340.03340.2462-0.05330.2556-0.0849-0.20510.04440.3336-0.030.01070.3173-0.06140.08343.347-41.61851.241
53.1850.5912-0.6911.39450.121.9003-0.04890.42180.0274-0.2573-0.01090.2095-0.0355-0.15460.05980.2339-0.032-0.03110.30370.01920.038210.533-45.5438.201
65.2624-3.0531-0.01768.99431.08615.57970.1315-0.3779-0.11240.4204-0.19260.61680.1483-0.06680.0610.3902-0.0658-0.00440.3913-0.06110.053913.145-39.48461.974
79.972-2.40062.80653.05954.01199.70370.18360.30690.4043-0.1662-0.2869-0.044-0.0883-0.24630.10330.3841-0.0196-0.03960.4561-0.01440.3974-1.337-52.95.249
85.53351.670.86655.20530.98732.5874-0.0136-0.39480.64220.0615-0.20570.08210.04450.27160.21930.3076-0.0652-0.02930.3684-0.02940.269742.58-32.73340.478
96.4932-4.6759-4.19518.23792.68523.35710.14650.53170.0993-0.168-0.28080.54360.1965-0.70220.13430.3191-0.05330.05340.4979-0.00290.2708-14.646-52.1540.446
100.82730.1449-2.27975.03311.90887.3989-0.06030.0071-0.0176-0.22820.1747-0.24040.04310.1584-0.11430.2876-0.02220.01750.2735-0.02560.11633.092-41.1865.283
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 205
2X-RAY DIFFRACTION2C1 - 205
3X-RAY DIFFRACTION3E1 - 205
4X-RAY DIFFRACTION4B1 - 205
5X-RAY DIFFRACTION5D1 - 205
6X-RAY DIFFRACTION6F1 - 17
7X-RAY DIFFRACTION7H1 - 17
8X-RAY DIFFRACTION8J1 - 17
9X-RAY DIFFRACTION9G1 - 17
10X-RAY DIFFRACTION10I1 - 17

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