[English] 日本語
Yorodumi
- PDB-6r8e: SC14 G-hairpin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r8e
TitleSC14 G-hairpin
ComponentsDNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3')
KeywordsDNA / G-hairpin DNA NMR spectroscopy structure dynamics
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsLenarcic Zivkovic, M. / Trantirek, L. / Plavec, J.
Funding support Slovenia, Czech Republic, 6items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-242 Slovenia
Slovenian Research AgencyJ1-6733 Slovenia
Ministry of Education (MoE, Czech Republic)MSCAfellow2@MUNI Czech Republic
Czech Science FoundationGA17-12075S Czech Republic
Czech Science Foundation19-26041X Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000477 Czech Republic
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Insight into formation propensity of pseudocircular DNA G-hairpins.
Authors: Zivkovic, M.L. / Gajarsky, M. / Bekova, K. / Stadlbauer, P. / Vicherek, L. / Petrova, M. / Fiala, R. / Rosenberg, I. / Sponer, J. / Plavec, J. / Trantirek, L.
History
DepositionApr 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)4,4141
Polymers4,4141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2770 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: DNA chain DNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3')


Mass: 4413.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D NOESY
222isotropic12D NOESY
272isotropic52D NOESY
161isotropic42D NOESY
232isotropic12D TOCSY
242isotropic22D DQF-COSY
151isotropic31D 15N-edited HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM / DNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3'), 90% H2O/10% D2OSC14_H2O90% H2O/10% D2O
solution20.6 mM / DNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3'), 100% D2OSC14_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMDNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3')/1
0.6 mMDNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3')/2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1120 mMH2O71 atm283 K
2120 mMD2O7.0 pD1 atm283 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III6005
Bruker AVANCE IIIBrukerAVANCE III8502
Bruker AVANCE IIIBrukerAVANCE III9504
Agilent DD2AgilentDD26003

-
Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
VNMRVarianprocessing
TopSpinBruker Biospinprocessing
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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