[English] 日本語
Yorodumi
- PDB-7e5p: Aptamer enhancing peroxidase activity of myoglobin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e5p
TitleAptamer enhancing peroxidase activity of myoglobin
ComponentsDNA (5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3')
KeywordsDNA / DNA aptamer parallel G-quadruplex myoglobin peroxidase activity enhancement
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsTsukakoshi, K. / Matsugami, A. / Khunathai, K. / Kanazashi, M. / Yamagishi, Y. / Nakama, K. / Oshikawa, D. / Hayashi, F. / Kuno, H. / Ikebukuro, K.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol.
Authors: Tsukakoshi, K. / Yamagishi, Y. / Kanazashi, M. / Nakama, K. / Oshikawa, D. / Savory, N. / Matsugami, A. / Hayashi, F. / Lee, J. / Saito, T. / Sode, K. / Khunathai, K. / Kuno, H. / Ikebukuro, K.
History
DepositionFeb 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 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*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,1311
Polymers5,1311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3')


Mass: 5131.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA aptamer / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY 500ms
121isotropic12D 1H-1H NOESY 50ms
131isotropic22D 1H-1H TOCSY 120ms
141isotropic22D DQF-COSY
151isotropic12D 1H-13C HSQC
162isotropic12D 1H-1H NOESY 50ms
172isotropic22D 1H-1H NOESY 250ms
182isotropic22D JR-HMBC
192isotropic12D 1H-15N HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM DNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'), 10 mM Potassium phosphate buffer pH 6.5, 100 uM DSS, 100% D2OD2O_sample100% D2O
solution21 mM DNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'), 10 mM Potassium phosphate buffer pH 6.5, 100 uM NA DSS, 95% H2O/5% D2OH2O_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3')natural abundance1
10 mMPotassium phosphate buffer pH 6.5natural abundance1
100 uMDSSnatural abundance1
1 mMDNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3')natural abundance2
10 mMPotassium phosphate buffer pH 6.5natural abundance2
100 uMDSSNA2
Sample conditionsIonic strength: 10 mM / Label: all_sample / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III8002

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.114Goddardpeak picking
TopSpin3.5Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
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://pdbjlvh1.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