[English] 日本語
Yorodumi
- PDB-7n43: Alpha-conotoxin OmIA with unusual pharmacological properties at a... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more