[English] 日本語
Yorodumi
- PDB-1kxl: Solution Structure of the Cdc13 DNA-binding Domain in a Complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kxl
TitleSolution Structure of the Cdc13 DNA-binding Domain in a Complex with Single-Stranded Telomeric DNA (DNA structure not modeled)
ComponentsCELL DIVISION CONTROL PROTEIN 13
KeywordsCELL CYCLE / DNA-binding domain / telomere / single-stranded DNA / OB fold
Function / homology
Function and homology information


negative regulation of DNA duplex unwinding / CST complex / ribonucleoprotein complex localization / telomerase inhibitor activity / translation elongation factor binding / regulation of telomere maintenance via telomerase / telomere capping / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding ...negative regulation of DNA duplex unwinding / CST complex / ribonucleoprotein complex localization / telomerase inhibitor activity / translation elongation factor binding / regulation of telomere maintenance via telomerase / telomere capping / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere maintenance via telomerase / telomere maintenance / chromosome, telomeric region / 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
Cell division control protein 13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsMitton-Fry, R.M. / Anderson, E.M. / Wuttke, D.S.
CitationJournal: Science / Year: 2002
Title: Conserved structure for single-stranded telomeric DNA recognition.
Authors: Mitton-Fry, R.M. / Anderson, E.M. / Hughes, T.R. / Lundblad, V. / Wuttke, D.S.
History
DepositionJan 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
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: CELL DIVISION CONTROL PROTEIN 13


Theoretical massNumber of molelcules
Total (without water)23,5751
Polymers23,5751
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)10 / 50structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #10closest to the average

-
Components

#1: Protein CELL DIVISION CONTROL PROTEIN 13


Mass: 23575.127 Da / Num. of mol.: 1 / Fragment: DNA-binding domain (residues 497-694)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32797

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1314D 13C/15N-separated NOESY
2424D 13C-separated NOESY
NMR detailsText: Representative conformer was structure closest to the mean.

-
Sample preparation

Details
Solution-IDSolvent system
190% H2O/10% D2O
2100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17ambient 303 K
27ambient 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002
Bruker DRXBrukerDRX8003

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglioprocessing
ANSIG3.3Kraulisdata analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
Details: DNA STRUCTURE NOT MODELED DUE TO CHEMICAL SHIFT ASSIGNMENT AMBIGUITY.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / 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