- 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
Title
Solution structure of DNA binding domain A (DBD-A) of S.cerevisiae Replication Protein A (RPA)
Components
Replication factor-A protein 1
Keywords
DNA BINDING PROTEIN / Canonical OB fold
Function / homology
Function and homology information
heteroduplex formation / sporulation / : / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / telomere maintenance via telomere lengthening / Removal of the Flap Intermediate / Translesion Synthesis by POLH / Activation of the pre-replicative complex / telomere maintenance via recombination ...heteroduplex formation / sporulation / : / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / telomere maintenance via telomere lengthening / Removal of the Flap Intermediate / Translesion Synthesis by POLH / Activation of the pre-replicative complex / telomere maintenance via recombination / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / mitotic recombination / Activation of ATR in response to replication stress / Termination of translesion DNA synthesis / reciprocal meiotic recombination / DNA unwinding involved in DNA replication / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA topological change / telomere maintenance via telomerase / Dual incision in TC-NER / 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 / nucleus / metal ion binding / 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
Replicationfactor-Aprotein1 / 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
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D 13C-separated NOESY
1
2
2
3D 15N-separated NOESY
NMR details
Text: The chemical shift assignments were done with triple-resonance experiments. Restraints were get from 3D 13C, 15N NOESY data.
Method: 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 representative
Selection criteria: lowest energy
NMR ensemble
Conformer 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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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