[English] 日本語
Yorodumi
- PDB-7pvb: Structure of Viscotoxin A3 from Viscum Album in the complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pvb
TitleStructure of Viscotoxin A3 from Viscum Album in the complex with DPC micelles
ComponentsViscotoxin-A3
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptides / viscotoxin / thionin / membrane activity / oligomerization / membrane disruption / cytotoxicity
Function / homologyThionin / Thionin-like superfamily / Plant thionin / Plant thionins signature. / defense response / toxin activity / extracellular region / Viscotoxin-A3
Function and homology information
Biological speciesViscum album (European mistletoe)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsParamonov, A.S. / Shenkarev, Z.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-30014 Russian Federation
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Spatial structure and oligomerization of viscotoxin A3 in detergent micelles: Implication for mechanisms of ion channel formation and membrane lysis.
Authors: Paramonov, A.S. / Lyukmanova, E.N. / Tonevitsky, A.G. / Arseniev, A.S. / Shenkarev, Z.O.
History
DepositionOct 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Viscotoxin-A3


Theoretical massNumber of molelcules
Total (without water)4,8431
Polymers4,8431
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study, NMR diffusion measurements reveal complex formation with DPC micelle
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

-
Components

#1: Protein/peptide Viscotoxin-A3


Mass: 4842.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P01538

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
122isotropic12D NOESY
141isotropic12D TOCSY
152isotropic12D 1H-13C HSQC
162isotropic12D DQF-COSY
171isotropic12D DQF-COSY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle11.6 mM VtA3, 128 mM [U-100% 2H] DPC, 95% H2O/5% D2Ovt_sample_h2o95% H2O/5% D2O
micelle21.6 mM VtA3, 128 mM [U-100% 2H] DPC, 100% D2Ovt_sample_D2o100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.6 mMVtA3natural abundance1
128 mMDPC[U-100% 2H]1
1.6 mMVtA3natural abundance2
128 mMDPC[U-100% 2H]2
Sample conditionsIonic strength: 10 mM / Ionic strength err: 1 / Label: cnd1 / pH: 4.0 / PH err: 0.1 / Pressure: AMBIENT atm / Temperature: 313 K / Temperature err: 0.1

-
NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
XEASY3.98.13Bartels et al.chemical shift assignment
CARAKeller and Wuthrichdata analysis
XEASYBartels et al.peak picking
VNMRVarianprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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