[English] 日本語
Yorodumi
- PDB-1emq: NMR OBSERVATION OF T-TETRADS IN A PARALLEL STRANDED DNA QUADRUPLE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1emq
TitleNMR OBSERVATION OF T-TETRADS IN A PARALLEL STRANDED DNA QUADRUPLEX FORMED BY SACCHAROMYCES CEREVISIAE TELOMERE REPEATS
ComponentsDNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3')
KeywordsDNA / T-tetrad / G-quadruplex / Telomere / Yeast / Saccharomyces cerevisiae
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / An initial model of quadruplex was generated on a IRIS workastation.Energy minimization by steepest descent, conjugate gradients methods was done using AMBER force field. Conformational search for the cquadruplex was performed by simulated annealing-reastarined molecular dynamics using AMBER forcefield. Relaxation matrix refinement was performed.
Model type detailsminimized average
AuthorsHosur, R.V. / Patel, P.K.
CitationJournal: Nucleic Acids Res. / Year: 1999
Title: NMR observation of T-tetrads in a parallel stranded DNA quadruplex formed by Saccharomyces cerevisiae telomere repeats.
Authors: Patel, P.K. / Hosur, R.V.
History
DepositionMar 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3')
B: DNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3')
C: DNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3')
D: DNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)8,6784
Polymers8,6784
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)1 / 8structures with the lowest energy
RepresentativeModel #1minimized average structure

-
Components

#1: DNA chain
DNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3')


Mass: 2169.433 Da / Num. of mol.: 4 / Fragment: YEAST TELOMERE REPEATS / Source method: obtained synthetically
Details: This sequence is two repeats of Saccharomyces cerevisiae telomere sequence

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121E-COSY
1312D-TOCSY
NMR detailsText: 0-70 C Temperature dependent one dimensional spectra. pH dependent spectra.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM DNA in 0.6 ml(90%H20/10%D2O) having 10 mM potassium phosphate, 0.2 mM EDTA, pH 7.0 and 100 mM KCl90% H2O/10% D2O
21-2 mM DNA in 0.6 ml(D2O) having 10 mM potassium phosphate, 0.2 mM EDTA, pH 7.0 and 100 mM KClD2O
Sample conditionspH: 7 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Bruker AMXBrukerAMX5002

-
Processing

NMR software
NameVersionDeveloperClassification
Felix230MSIprocessing
VNMR6.1Variancollection
Discover3.1MSIstructure solution
IRMA2.3MSIrefinement
RefinementMethod: An initial model of quadruplex was generated on a IRIS workastation.Energy minimization by steepest descent, conjugate gradients methods was done using AMBER force field. Conformational ...Method: An initial model of quadruplex was generated on a IRIS workastation.Energy minimization by steepest descent, conjugate gradients methods was done using AMBER force field. Conformational search for the cquadruplex was performed by simulated annealing-reastarined molecular dynamics using AMBER forcefield. Relaxation matrix refinement was performed.
Software ordinal: 1
Details: A total of 234 NOEs constarint. 20 hydrogen bonds constraints. 8 convergant structure after IRMA refinement. R1 factor = 0.31-0.33. r.m.s.d.s from average structure 0.2-0.4. Nil violation exceeding 0.2 A.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 8 / Conformers submitted total number: 1

+
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