[English] 日本語
Yorodumi
- PDB-1ynx: Solution structure of DNA binding domain A (DBD-A) of S.cerevisia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ynx
TitleSolution structure of DNA binding domain A (DBD-A) of S.cerevisiae Replication Protein A (RPA)
ComponentsReplication factor-A protein 1
KeywordsDNA BINDING PROTEIN / Canonical OB fold
Function / homology
Function and homology information


heteroduplex formation / sporulation / DNA replication factor A complex / telomere maintenance via telomere lengthening / telomere maintenance via recombination / mitotic recombination / reciprocal meiotic recombination / DNA unwinding involved in DNA replication / DNA topological change / telomere maintenance via telomerase ...heteroduplex formation / sporulation / DNA replication factor A complex / telomere maintenance via telomere lengthening / telomere maintenance via recombination / mitotic recombination / reciprocal meiotic recombination / DNA unwinding involved in DNA replication / DNA topological change / telomere maintenance via telomerase / telomere maintenance / condensed nuclear chromosome / nucleotide-excision repair / double-strand break repair via homologous recombination / establishment of protein localization / single-stranded DNA binding / double-stranded DNA binding / DNA replication / sequence-specific DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / mRNA binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins ...Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Replication factor A protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / Torsional Angle Dynamics with Internal Variable Module
AuthorsPark, C.J. / Lee, J.H. / Choi, B.S.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen
Authors: Park, C.J. / Lee, J.H. / Choi, B.S.
History
DepositionJan 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Replication factor-A protein 1


Theoretical massNumber of molelcules
Total (without water)13,2661
Polymers13,2661
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)22 / 100structures with the lowest energy
RepresentativeModel #12lowest energy

-
Components

#1: Protein Replication factor-A protein 1 / Replication Protein A / RF-A / Single-stranded DNA-binding protein / DNA binding protein BUF2 / ...Replication Protein A / RF-A / Single-stranded DNA-binding protein / DNA binding protein BUF2 / Replication protein A 69 kDa DNA- binding subunit


Mass: 13265.821 Da / Num. of mol.: 1 / Fragment: DNA binding domain A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RFA1 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P22336

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
NMR detailsText: The chemical shift assignments were done with triple-resonance experiments. Restraints were get from 3D 13C, 15N NOESY data.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM scRPA DBD A U-15N, 13C; 20mM Sodium Phosphate, 100mM NaCl, 2mM DTT, pH 7.0; 90% H2O, 10% D2O90% H2O/10% D2O
21mM scRPA DBD A U-15N; 20mM Sodium Phosphate, 100mM NaCl, 2mM DTT, pH 7.0; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipelatestDelaglio et al.processing
VNMRlatestVarian, Inc.collection
X-PLORNIH 2.9.6Clore et al.,structure solution
X-PLORNIH 2.9.6Clore et al.,refinement
RefinementMethod: Torsional Angle Dynamics with Internal Variable Module
Software ordinal: 1
Details: The structure calculations were performed using 1138 interproton distance restraints and 161 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 22

+
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