[English] 日本語
Yorodumi
- PDB-5tcz: NMR solution structure of engineered Protoxin-II analog -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tcz
TitleNMR solution structure of engineered Protoxin-II analog
ComponentsBeta/omega-theraphotoxin-Tp2a
KeywordsTOXIN / venom peptide analog / inhibitor / cystine knot
Function / homologycalcium channel regulator activity / sodium channel regulator activity / toxin activity / lipid binding / extracellular region / Beta/omega-theraphotoxin-Tp2a
Function and homology information
Biological speciesThrixopelma pruriens (green velvet)
MethodSOLUTION NMR / simulated annealing
AuthorsGibbs, A.C. / Wickenden, A.D.
CitationJournal: Sci Rep / Year: 2017
Title: Insensitivity to pain induced by a potent selective closed-state Nav1.7 inhibitor.
Authors: Flinspach, M. / Xu, Q. / Piekarz, A.D. / Fellows, R. / Hagan, R. / Gibbs, A. / Liu, Y. / Neff, R.A. / Freedman, J. / Eckert, W.A. / Zhou, M. / Bonesteel, R. / Pennington, M.W. / Eddinger, K. ...Authors: Flinspach, M. / Xu, Q. / Piekarz, A.D. / Fellows, R. / Hagan, R. / Gibbs, A. / Liu, Y. / Neff, R.A. / Freedman, J. / Eckert, W.A. / Zhou, M. / Bonesteel, R. / Pennington, M.W. / Eddinger, K.A. / Yaksh, T.L. / Hunter, M. / Swanson, R.V. / Wickenden, A.D.
History
DepositionSep 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta/omega-theraphotoxin-Tp2a


Theoretical massNumber of molelcules
Total (without water)3,8631
Polymers3,8631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3120 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Beta/omega-theraphotoxin-Tp2a


Mass: 3862.721 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thrixopelma pruriens (green velvet) / References: UniProt: P83476*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC

-
Sample preparation

DetailsType: solution / Contents: 1.51 mM JNJ63955918, 90% H2O/10% D2O / Label: 1H_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.51 mM / Component: JNJ63955918 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 6.7 / Pressure: 1 atm / Temperature: 305.56 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 950 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
MOE2015.1Chemical Computing Grouprefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
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://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