[English] 日本語
Yorodumi
- PDB-6px7: Dg12a in Weaponisation 'on the fly': Convergent recruitment of kn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6px7
TitleDg12a in Weaponisation 'on the fly': Convergent recruitment of knottin and defensin scaffolds as neurotoxins in the venom of assassin fly Dolopus genitalis (Diptera: Asilidae)
ComponentsVenom polypeptide
KeywordsTOXIN / disulfide-rich / assassin-fly / knottin / ultra-stable peptide
Function / homologyion channel regulator activity / toxin activity / extracellular region / U-Asilidin(1)-Dg12
Function and homology information
Biological speciesDolopus genitalis (fry)
MethodSOLUTION NMR / simulated annealing
AuthorsAgwa, A.J. / Schroeder, C.
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2019
Title: Weaponisation 'on the fly': Convergent recruitment of knottin and defensin peptide scaffolds into the venom of predatory assassin flies.
Authors: Jin, J. / Agwa, A.J. / Szanto, T.G. / Csoti, A. / Panyi, G. / Schroeder, C.I. / Walker, A.A. / King, G.F.
History
DepositionJul 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 20, 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 / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Venom polypeptide


Theoretical massNumber of molelcules
Total (without water)3,9231
Polymers3,9231
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 / 20structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein/peptide Venom polypeptide


Mass: 3922.558 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dolopus genitalis (fry) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G5BIC2
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-1H TOCSY
121anisotropic12D 1H-1H NOESY
131anisotropic12D 1H-15N HSQC
141anisotropic12D 1H-13C HSQC
151anisotropic12D 1H-1H COSY

-
Sample preparation

DetailsType: solution / Contents: 1 mg/mL Dg12a, 90% H2O/10% D2O / Details: Peptide / Label: Dg12a / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mg/mL / Component: Dg12a / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 1 M / Label: Dg12a / pH: 4 / Pressure: 1 Pa / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospinrefinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis2.4.1CCPNchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / 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