[English] 日本語
Yorodumi
- PDB-8fd4: Solution structure of mu-theraphotoxin Cg4a from Chinese tarantul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fd4
TitleSolution structure of mu-theraphotoxin Cg4a from Chinese tarantula Chilobrachys jingzhao
ComponentsJingzhaotoxin F7-10.36
KeywordsTOXIN / peptide / spider toxin / voltage-gated sodium channel modulator
Function / homologyHuwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / toxin activity / extracellular region / Jingzhaotoxin F7-10.36
Function and homology information
Biological speciesChilobrachys guangxiensis (spider)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSharma, G. / Jia, X. / Chin, Y.K.Y. / Mobli, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: Solution structure of mu-theraphotoxin Cg4a from Chinese tarantula Chilobrachys jingzhao
Authors: Sharma, G. / Deuis, J. / Rahnama, S. / Jia, X. / Chin, Y.K.Y. / Undheim, E.A.B. / Vetter, I. / Mobli, M.
History
DepositionDec 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Jingzhaotoxin F7-10.36


Theoretical massNumber of molelcules
Total (without water)3,9431
Polymers3,9431
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

-
Components

#1: Protein/peptide Jingzhaotoxin F7-10.36 / Peptide F7-10.36 / Mu-theraphotoxin Cg4a


Mass: 3942.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chilobrachys guangxiensis (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: P0CH54

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic12D 1H-15N HSQC
131isotropic13D 1H-13C NOESY aliphatic
141isotropic13D 1H-13C NOESY aromatic
151isotropic13D 1H-15N NOESY
171isotropic13D HN(CA)CB
191isotropic13D CBCA(CO)NH
181isotropic13D H(CCO)NH
161isotropic13D C(CO)NH
1101isotropic13D HNCO
1111isotropic13D HBHA(CO)NH

-
Sample preparation

DetailsType: solution
Contents: 340 uM [U-100% 13C; U-100% 15N] Mu-theraphotoxin Cg4a, 20 mM sodium acetate, 5 % [U-2H] D2O, 95% H2O/5% D2O
Label: CN-Cg4a / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
340 uMMu-theraphotoxin Cg4a[U-100% 13C; U-100% 15N]1
20 mMsodium acetatenatural abundance1
5 %D2O[U-2H]1
Sample conditionsIonic strength: 20 mM / Label: condition1 / pH: 5 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 900 MHz

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
TopSpinBruker Biospincollection
TALOS-NProtein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks Y. Shen and A. Bax J Biomol NMR 2013 Vol. 56 Issue 3 Pages 227-41geometry optimization
TopSpinBruker Biospinprocessing
Rowland NMR Toolkit (RNMRTK)http://rnmrtk.uchc.edu/rnmrtk/RNMRTK. htmlprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / 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