[English] 日本語
Yorodumi
- PDB-6vxw: NMR solution structure of natural scorpion toxin Cl13 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vxw
TitleNMR solution structure of natural scorpion toxin Cl13
ComponentsBeta-toxin Cl13
KeywordsTOXIN / sodium beta toxin
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular region
Similarity search - Function
Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCentruroides limpidus (Mexican scorpion)
MethodSOLUTION NMR / simulated annealing
Authorsdel Rio Portilla, F. / Delepierre, M. / Lopez Giraldo, A.E.
CitationJournal: Toxicon / Year: 2020
Title: The three-dimensional structure of the toxic peptide Cl13 from the scorpion Centruroides limpidus.
Authors: Lopez-Giraldo, A.E. / Olamendi-Portugal, T. / Riano-Umbarila, L. / Becerril, B. / Possani, L.D. / Delepierre, M. / Del Rio-Portilla, F.
History
DepositionFeb 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-toxin Cl13


Theoretical massNumber of molelcules
Total (without water)7,8661
Polymers7,8661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein Beta-toxin Cl13


Mass: 7866.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Centruroides limpidus (Mexican scorpion) / References: UniProt: C0HK69
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
211isotropic12D 1H-1H TOCSY
221isotropic12D 1H-1H NOESY
231isotropic12D DQF-COSY
141isotropic22D 1H-1H TOCSY
251isotropic22D 1H-1H TOCSY
361isotropic22D 1H-1H TOCSY
481isotropic22D 1H-1H TOCSY
571isotropic22D 1H-1H TOCSY
1131isotropic22D 1H-1H NOESY
2121isotropic22D 1H-1H NOESY
3111isotropic22D 1H-1H NOESY
4101isotropic22D 1H-1H NOESY
591isotropic22D 1H-1H NOESY
1181isotropic22D DQF-COSY
2171isotropic22D DQF-COSY
3161isotropic22D DQF-COSY
4151isotropic22D DQF-COSY
5141isotropic22D DQF-COSY
2221isotropic12D 1H-15N HSQC
2211isotropic12D 1H-13C HSQC
2201isotropic113C HSQCTOCSY
2191isotropic113C HMBC

-
Sample preparation

DetailsType: solution / Contents: 2.5 mM Cl13, 95% H2O/5% D2O / Label: Nat. ab. / Solvent system: 95% H2O/5% D2O
SampleConc.: 2.5 mM / Component: Cl13 / Isotopic labeling: natural abundance
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1Acetate buffer at 20 mM20 mMA4.71 atm288 K
220 mMB4.71 atm298 K
320 mMC4.71 atm303 K
420 mMD4.71 atm313 K
520 mME4.71 atm318 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE8001CRYOPROBE
Bruker AVANCE IIIBrukerAVANCE III6002CRYOPROBE

-
Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARA1.5Keller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
TALOSNCornilescu, Delaglio and Baxchemical shift calculation
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 500 / Conformers submitted total number: 20

+
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