[English] 日本語
Yorodumi
- PDB-2aqy: (3+1) assembly of three human telomeric DNA repeats into an asymm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2aqy
Title(3+1) assembly of three human telomeric DNA repeats into an asymmetrical dimeric G-quadruplex
Components
  • 5'-D(*GP*(OIP)P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*T)-3'
  • 5'-D(*TP*AP*GP*GP*GP*(DU))-3'
KeywordsDNA / (3+1) G-quadruplex assembly / asymmetric dimeric G-quadruplex / telomeric DNA.
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics matrix relaxation
AuthorsZhang, N. / Phan, A.T. / Patel, D.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: (3 + 1) Assembly of three human telomeric repeats into an asymmetric dimeric G-quadruplex
Authors: Zhang, N. / Phan, A.T. / Patel, D.J.
History
DepositionAug 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*GP*(OIP)P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*T)-3'
B: 5'-D(*TP*AP*GP*GP*GP*(DU))-3'


Theoretical massNumber of molelcules
Total (without water)6,9002
Polymers6,9002
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #1lowest energy

-
Components

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


Mass: 5050.259 Da / Num. of mol.: 1 / Fragment: three repeats of human telomeric DNA / Mutation: G2(OIP) / Source method: obtained synthetically
Details: This sequence occurs naturally in homo sapiens (human).
#2: DNA chain 5'-D(*TP*AP*GP*GP*GP*(DU))-3'


Mass: 1850.226 Da / Num. of mol.: 1 / Fragment: single repeats of human telomeric DNA / Mutation: T22(DU) / Source method: obtained synthetically / Details: T22(DU) mutation

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1322D TOCSY
142DQF-COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
1100mM NaCl, 2mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
2100mM NaCl, 2mM phosphate buffer, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM Na+ 6.8 1 atm303 K
2100mM Na+ 6.8 1 atm273 K
3100mM Na+ 6.8 1 atm283 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerrefinement
Felix2000MSIdata analysis
RefinementMethod: distance geometry simulated annealing, molecular dynamics matrix relaxation
Software ordinal: 1
Details: Additional comments about the NMR refinement can be placed here, e.g. the structures are based on a total of 517 restraints, 466 are NOE-derived distance constraints, 22 dihedral angle ...Details: Additional comments about the NMR refinement can be placed here, e.g. the structures are based on a total of 517 restraints, 466 are NOE-derived distance constraints, 22 dihedral angle restraints,51 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable ...Conformer selection criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 10 / 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