[English] 日本語
Yorodumi
- PDB-2myh: Omega-Tbo-IT1: selective inhibitor of insect calcium channels iso... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2myh
TitleOmega-Tbo-IT1: selective inhibitor of insect calcium channels isolated from Tibellus oblongus spider venom
ComponentsOmega-Tbo-IT1 toxin
KeywordsTOXIN / cystine knot inhibitor / ICK
Function / homologytoxin activity / extracellular region / Omega-phylotoxin-To1a
Function and homology information
Biological speciesTibellus oblongus (spider)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsAltukhov, D. / Bozin, T. / Bocharov, E. / Kozlov, S. / Mikov, A.
CitationJournal: Sci Rep / Year: 2015
Title: omega-Tbo-IT1-New Inhibitor of Insect Calcium Channels Isolated from Spider Venom.
Authors: Mikov, A.N. / Fedorova, I.M. / Potapieva, N.N. / Maleeva, E.E. / Andreev, Y.A. / Zaitsev, A.V. / Kim, K.K. / Bocharov, E.V. / Bozin, T.N. / Altukhov, D.A. / Lipkin, A.V. / Kozlov, S.A. / ...Authors: Mikov, A.N. / Fedorova, I.M. / Potapieva, N.N. / Maleeva, E.E. / Andreev, Y.A. / Zaitsev, A.V. / Kim, K.K. / Bocharov, E.V. / Bozin, T.N. / Altukhov, D.A. / Lipkin, A.V. / Kozlov, S.A. / Tikhonov, D.B. / Grishin, E.V.
History
DepositionJan 23, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Omega-Tbo-IT1 toxin


Theoretical massNumber of molelcules
Total (without water)4,3481
Polymers4,3481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

-
Components

#1: Protein/peptide Omega-Tbo-IT1 toxin


Mass: 4348.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tibellus oblongus (spider) / Plasmid: pET-32-b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0G3F8Z3*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: TWO-DIMENSIONAL 1H-1H DQF-COSY, TOCSY (80-MS MIXING TIME), NOESY (120-MS MIXING TIME) AND 1H-13C HSQC (AT NATURAL ABUNDANCE) NMR SPECTRA OF 1.5 MM RECOMBINANT OMEGA-TBO-IT1 TOXIN ...Details: TWO-DIMENSIONAL 1H-1H DQF-COSY, TOCSY (80-MS MIXING TIME), NOESY (120-MS MIXING TIME) AND 1H-13C HSQC (AT NATURAL ABUNDANCE) NMR SPECTRA OF 1.5 MM RECOMBINANT OMEGA-TBO-IT1 TOXIN (SOLUBILIZED IN H2O OR D2O WITH 20 MM PHOSPHATE BUFFER, PH 5.8) WERE ACQUIRED AT 12C AND 20C ON NMR SPECTROMETER VARIAN NMR SYSTEM 700 MHZ.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-13C HSQC
1422D DQF-COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM Omega-Tbo-IT1, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM Omega-Tbo-IT1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.5 mMOmega-Tbo-IT1-11
1.5 mMOmega-Tbo-IT1-22
Sample conditionsIonic strength: 0.06 / pH: 5.8 / Pressure: ambient / Temperature: 285 K

-
NMR measurement

NMR spectrometerType: Varian Uniform NMR System 700 / Manufacturer: Varian / Model: Uniform NMR System 700 / Field strength: 700 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
ACMEDelaglio, Zhengrong and Baxprocessing
MolmolKoradi, Billeter and Wuthrichprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 422 / NOE intraresidue total count: 249 / NOE long range total count: 49 / NOE medium range total count: 21 / NOE sequential total count: 103 / Disulfide bond constraints total count: 24 / Hydrogen bond constraints total count: 88 / Protein chi angle constraints total count: 89 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 89 / Protein psi angle constraints total count: 2
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / 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://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