[English] 日本語
Yorodumi
- PDB-1c34: SOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMIDIATE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c34
TitleSOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMIDIATE
ComponentsDNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
KeywordsDNA / APTAMER / THROMBIN BINDING / POTASSIUM / METAL BINDING SITES / QUADRUPLEX / INTERMEDIATE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / STRUCTURE REFINEMENT OF THE DNA WAS PREFORMED USING COMPLETE RELAXATION MATRIX, RESTRAINED MOLECULAR DYNAMICS.
AuthorsBolton, P.H. / Marathias, V.M. / Wang, K.
Citation
Journal: Nucleic Acids Res. / Year: 2000
Title: Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA.
Authors: Marathias, V.M. / Bolton, P.H.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Determination of the Number and Location of the Manganese Binding Sites of DNA Quadruplexes in Solution by EPR and NMR in the Presence and Absence of Thrombin
Authors: Bolton, P.H. / Marathias, V.M. / Wang, K.
History
DepositionJul 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 1999Provider: 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(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,7431
Polymers4,7431
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)11 / 1180 TO 100PS STRUCTURES FROM DYNAMICS
Representative

-
Components

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


Mass: 4743.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THROMBIN BINDING APTAMER INTERMIDIATE

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121PE-COSY
131ROESY
141BASD-TOCSY
1522D NOESY
NMR detailsText: THIS STRUCTURE IS THE INTERMEDIATE FORM OF THE 15MER QUADRUPLEX WITH ONLY 1 POTASSSIUM PER DNA MOLECULE.

-
Sample preparation

Details
Solution-IDContents
1140 MM NACL, 1.4 MM KCL, 20 MM TRISD11 PH=7.0
2140 MM NACL, 1.4 MM KCL, 20 MM TRISD11 PH=7.0
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1140 mM NACL, 71 atm288 K
2140 mM NACL, 71 atm278 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian UNITYPLUSVarianUNITYPLUS4002

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVARIANcollection
VNMR6.1BVARIANprocessing
Felix970MSIprocessing
Felix970MSIrefinement
X-PLOR3.1BRUNGERstructure solution
X-PLOR3.1BRUNGERrefinement
RefinementMethod: STRUCTURE REFINEMENT OF THE DNA WAS PREFORMED USING COMPLETE RELAXATION MATRIX, RESTRAINED MOLECULAR DYNAMICS.
Software ordinal: 1
NMR ensembleConformer selection criteria: 80 TO 100PS STRUCTURES FROM DYNAMICS
Conformers calculated total number: 11 / Conformers submitted total number: 11

+
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