[English] 日本語
Yorodumi
- PDB-1s40: SOLUTION STRUCTURE OF THE CDC13 DNA-BINDING DOMAIN COMPLEXED WITH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s40
TitleSOLUTION STRUCTURE OF THE CDC13 DNA-BINDING DOMAIN COMPLEXED WITH A SINGLE-STRANDED TELOMERIC DNA 11-MER
Components
  • 5'-D(*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G)-3'
  • Cell division control protein 13
KeywordsCELL CYCLE/DNA / ssDNA / single-stranded nucleic acid / recognition / specificity / cdc13 / OB-fold / telomere / CELL CYCLE-DNA COMPLEX
Function / homology
Function and homology information


ribonucleoprotein complex localization / CST complex / telomerase inhibitor activity / translation elongation factor binding / regulation of telomere maintenance via telomerase / nuclear telomere cap complex / G-rich strand telomeric DNA binding / single-stranded telomeric DNA binding / telomere capping / telomere maintenance via telomerase ...ribonucleoprotein complex localization / CST complex / telomerase inhibitor activity / translation elongation factor binding / regulation of telomere maintenance via telomerase / nuclear telomere cap complex / G-rich strand telomeric DNA binding / single-stranded telomeric DNA binding / telomere capping / telomere maintenance via telomerase / telomere maintenance / chromosome, telomeric region / cell cycle / cell division / identical protein binding
Similarity search - Function
Cell division control protein 13, OB2 domain / Cell division control protein 13, OB2 domain / Cell division control protein 13, N-terminal / Cdc13, OB4 dimerization domain / Cell division control protein 13 N-terminus / Cdc13 OB4 dimerization domain / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 ...Cell division control protein 13, OB2 domain / Cell division control protein 13, OB2 domain / Cell division control protein 13, N-terminal / Cdc13, OB4 dimerization domain / Cell division control protein 13 N-terminus / Cdc13 OB4 dimerization domain / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Cell division control protein 13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics
AuthorsMitton-Fry, R.M. / Anderson, E.M. / Theobald, D.L. / Glustrom, L.W. / Wuttke, D.S.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural basis for telomeric single-stranded DNA recognition by yeast Cdc13
Authors: Mitton-Fry, R.M. / Anderson, E.M. / Theobald, D.L. / Glustrom, L.W. / Wuttke, D.S.
History
DepositionJan 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 5'-D(*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G)-3'
A: Cell division control protein 13


Theoretical massNumber of molelcules
Total (without water)27,0512
Polymers27,0512
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 / 100structures with acceptable covalent geometry, structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

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


Mass: 3476.254 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Cell division control protein 13


Mass: 23575.127 Da / Num. of mol.: 1 / Fragment: DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC13, YDL220C / Production host: Escherichia coli (E. coli) / References: UniProt: P32797

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
1333D 13C-separated NOESY
1444D 13C/15N-separated NOESY
1554D 13C-separated NOESY
166Isotope filtered NOESY
177Select-filtered NOESY
NMR detailsText: Models superimposed using Douglas Theobald's THESEUS program for multiple superpositions, variance-weighted simultaneous superpositioning. The final weighted RMSD from the mean is 0.64152A over ...Text: Models superimposed using Douglas Theobald's THESEUS program for multiple superpositions, variance-weighted simultaneous superpositioning. The final weighted RMSD from the mean is 0.64152A over all alpha-carbon atoms

-
Sample preparation

DetailsContents: 0.8-1.5mM unlabeled, 15N-labeled or 13C,15N-labeled protein; 0.9-1.7mM ssDNA; 50mM imidazole-d4, pH or pD* 7.0; 150mM NaCl; 100mM Na2SO4; 0.02% NaN3; 2mM DTT-d10 in 10% D2O/90% H2O or 100% D2O
Solvent system: 10% D2O/90% H2O or 100% D2O
Sample conditionsIonic strength: 150mM NaCl, 100mM Na2SO4 / pH: 7.0 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY6001
Varian UNITYVarianUNITY5002
Bruker DRXBrukerDRX8003

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxdata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, 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://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