[English] 日本語
Yorodumi
- PDB-2axk: Solution structure of discrepin, a scorpion venom toxin blocking ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2axk
TitleSolution structure of discrepin, a scorpion venom toxin blocking K+ channels.
Componentsdiscrepin
KeywordsTOXIN / discrepin / scorpion toxin / A-current / K+-channel
Function / homology
Function and homology information


envenomation resulting in negative regulation of platelet aggregation in another organism / potassium channel inhibitor activity / : / toxin activity / extracellular region
Similarity search - Function
Scorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily
Similarity search - Domain/homology
Potassium channel toxin alpha-KTx 15.6
Similarity search - Component
MethodSOLUTION NMR / torsion angle dynamics
AuthorsProchnicka-Chalufour, A. / Corzo, G. / Satake, H. / Martin-Eauclaire, M.-F. / Murgia, A.R. / Prestipino, G. / D'Suze, G. / Possani, L.D. / Delepierre, M.
Citation
Journal: Biochemistry / Year: 2006
Title: Solution structure of discrepin, a new K+-channel blocking peptide from the alpha-KTx15 subfamily.
Authors: Prochnicka-Chalufour, A. / Corzo, G. / Satake, H. / Martin-Eauclaire, M.-F. / Murgia, A.R. / Prestipino, G. / D'Suze, G. / Possani, L.D. / Delepierre, M.
#1: Journal: Arch.Biochem.Biophys. / Year: 2004
Title: Discrepin, a new peptide of the sub-family alpha-ktx15, isolated from the scorpion Tityus discrepans irreversibly blocks K+-channels (IA currents) of cerebellum granular cells.
Authors: D'Suze, G. / Batista, C.V.F. / Frau, A. / Murgia, A.R. / Zamudio, F.Z. / Sevcik, C. / Possani, L.D. / Prestipino, G.
History
DepositionSep 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_assembly ...entity_poly / pdbx_struct_assembly / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE No suitable sequence database reference was available at the time of processing this file.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: discrepin


Theoretical massNumber of molelcules
Total (without water)4,1901
Polymers4,1901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy and best secondary structure
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide discrepin


Mass: 4189.889 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in the venom of scorpion Tityus discrepans.
References: UniProt: P84777

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222Q-COSY
1312D NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
13 mM discrepin 10% D2O90% H2O/10% D2O
23 mM discrepin 100% D2O100% D2O
Sample conditionsIonic strength: 5 / pH: 4 / Pressure: ambient / Temperature: 308 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian Inc.collection
XEASY3.1Bartels et al.data analysis
ARIA1.2Nilges et al.structure solution
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: structures based on total of 565 meaningful distance constraints, 22 dihedral angle constraints and three hydrogen bonds. Three disulfide bridges (8-29, 14-34, 18-36) were also included in caclulation.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy and best secondary structure
Conformers calculated total number: 200 / Conformers submitted total number: 10

+
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://pdbjlvh1.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