[English] 日本語
Yorodumi
- PDB-6sx6: Guanine-rich oligonucleotide with 5'-GC end form G-quadruplex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sx6
TitleGuanine-rich oligonucleotide with 5'-GC end form G-quadruplex with A(GGGG)A hexad, GCGC- and G-quartets and two symmetric GG and AA base pairs
ComponentsGCn
KeywordsDNA / G-quadruplex / A(GGGG)A hexad / GCGC-quartet / 5'-GC ends
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsPavc, D. / Wang, B. / Spindler, L. / Drevensek-Olenik, I. / Plavec, J. / Sket, P.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research Agency Slovenia
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly.
Authors: Pavc, D. / Wang, B. / Spindler, L. / Drevensek-Olenik, I. / Plavec, J. / Sket, P.
History
DepositionSep 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GCn
B: GCn


Theoretical massNumber of molelcules
Total (without water)7,6672
Polymers7,6672
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1440 Å2
ΔGint2 kcal/mol
Surface area3980 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: DNA chain GCn


Mass: 3833.490 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
212isotropic12D NOESY
222isotropic22D NOESY
333isotropic12D NOESY
343isotropic22D NOESY
363isotropic22D TOCSY
272isotropic22D DQF-COSY
383isotropic22D 1H-31P COSY
191isotropic22D 1H-13C HSQC aromatic

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM 8% 13C, 8% 15N GCN, 100 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2OSite-specific 13C,15N labelled samples used for unambiguous assignment.13C15N_sample90% H2O/10% D2O
solution21 mM GCN, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2Ounlabelled_sample90% H2O/10% D2O
solution31 mM GCN, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2Ounlabelled_sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMGCN8% 13C, 8% 15N1
100 mMsodium chloridenatural abundance1
10 mMsodium phosphate buffernatural abundance1
1 mMGCNnatural abundance2
175 mMsodium chloridenatural abundance2
10 mMsodium phosphate buffernatural abundance2
1 mMGCNnatural abundance3
175 mMsodium chloridenatural abundance3
10 mMsodium phosphate buffernatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mM13C15N_sample_conditions6.8 1 atm298 K
2175 mMunlabelled_sample_conditions6.8 1 atm298 K
3175 mMunlabelled_sample_D2O_conditions6.8 1 atm298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent Agilent Technologies VNMRS 800 MHz NMR spectrometerAgilentAgilent Technologies VNMRS 800 MHz NMR spectrometer8001
Agilent Agilent Technologies DD2 600 MHz NMR spectrometerAgilentAgilent Technologies DD2 600 MHz NMR spectrometer6002

-
Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
VNMRVarianprocessing
VNMRVarianchemical shift assignment
SparkyGoddardpeak picking
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / 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