[English] 日本語
Yorodumi
- PDB-2knm: Solution structure of the cyclotide cycloviolacin O2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2knm
TitleSolution structure of the cyclotide cycloviolacin O2
ComponentsCycloviolacin-O2
KeywordsPLANT PROTEIN / cyclotide / cyclic cystine knot / circular protein / Cytolysis / Disulfide bond / Hemolysis / Knottin / Plant defense
Function / homologyCyclotide, bracelet, conserved site / Cyclotides bracelet subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / defense response / killing of cells of another organism / Cycloviolacin-O2
Function and homology information
Biological speciesViola odorata (plant)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsRosengren, K.
CitationJournal: Chembiochem / Year: 2009
Title: The conserved glu in the cyclotide cycloviolacin O2 has a key structural role.
Authors: Goransson, U. / Herrmann, A. / Burman, R. / Haugaard-Jonsson, L.M. / Rosengren, K.J.
History
DepositionAug 27, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cycloviolacin-O2


Theoretical massNumber of molelcules
Total (without water)3,1681
Polymers3,1681
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Cycloviolacin-O2


Mass: 3167.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viola odorata (plant) / References: UniProt: P58434
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR solution structure of the cytotoxic cyclotide cycloviolacin O2 isolated from Viola odorata. This peptide is naturally head-to-tail cyclic, i.e. has a peptide bond between the N- and C-termini.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY
1422D 1H-1H TOCSY
1522D 1H-1H NOESY
1612D 1H-1H TOCSY
1712D 1H-1H NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM cycloviolacin O2, 90% H2O/10% D2O90% H2O/10% D2O
21-2 mM cycloviolacin O2, 100% D2O100% D2O
Sample
UnitsComponentConc. range (mg/ml)Solution-ID
mMcycloviolacin O2-11-21
mMcycloviolacin O2-21-22
Sample conditionspH: 6.1 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian AvanceVarianAVANCE5002

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
VNMR6.1Varianprocessing
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichchemical shift assignment
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures were calculated using torsion angle dynamics within CNS and subsequently refined and energy minimised using cartesian dynamics in explicit water.
NMR constraintsNOE constraints total: 155 / NOE intraresidue total count: 0 / NOE long range total count: 38 / NOE medium range total count: 31 / NOE sequential total count: 86 / Hydrogen bond constraints total count: 32 / Protein chi angle constraints total count: 9 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 14 / Protein psi angle constraints total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.273 Å

+
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