[English] 日本語
Yorodumi
- PDB-1fhr: SOLUTION STRUCTURE OF THE FHA2 DOMAIN OF RAD53 COMPLEXED WITH A P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fhr
TitleSOLUTION STRUCTURE OF THE FHA2 DOMAIN OF RAD53 COMPLEXED WITH A PHOSPHOTYROSYL PEPTIDE
Components
  • DNA REPAIR PROTEIN RAD9
  • PROTEIN KINASE SPK1
KeywordsTRANSFERASE / FHA domain / Rad53 / Rad9 / phosphotyrosine / phosphoprotein
Function / homology
Function and homology information


negative regulation of DNA strand resection involved in replication fork processing / deoxyribonucleoside triphosphate biosynthetic process / G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / meiotic recombination checkpoint signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of transcription factors / negative regulation of phosphorylation / dual-specificity kinase ...negative regulation of DNA strand resection involved in replication fork processing / deoxyribonucleoside triphosphate biosynthetic process / G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / meiotic recombination checkpoint signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of transcription factors / negative regulation of phosphorylation / dual-specificity kinase / mitotic intra-S DNA damage checkpoint signaling / DNA replication origin binding / negative regulation of DNA damage checkpoint / DNA replication initiation / enzyme activator activity / regulation of DNA repair / mitotic G1 DNA damage checkpoint signaling / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / nucleotide-excision repair / protein localization / double-strand break repair / histone binding / double-stranded DNA binding / protein tyrosine kinase activity / regulation of cell cycle / protein kinase activity / phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Rad9-like Rad53-binding domain, fungi / Fungal Rad9-like Rad53-binding / Serine/threonine-protein kinase Rad53 / : / : / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain ...Rad9-like Rad53-binding domain, fungi / Fungal Rad9-like Rad53-binding / Serine/threonine-protein kinase Rad53 / : / : / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA repair protein RAD9 / Serine/threonine-protein kinase RAD53
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsByeon, I.-J.L. / Liao, H. / Yongkiettrakul, S. / Tsai, M.-D.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: II. Structure and specificity of the interaction between the FHA2 domain of Rad53 and phosphotyrosyl peptides.
Authors: Wang, P. / Byeon, I.J. / Liao, H. / Beebe, K.D. / Yongkiettrakul, S. / Pei, D. / Tsai, M.D.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Structure and function of a new phosphopeptide-binding domain containing the FHA2 of Rad53
Authors: Liao, H. / Byeon, I.-J.L. / Tsai, M.-D.
History
DepositionAug 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN KINASE SPK1
P: DNA REPAIR PROTEIN RAD9


Theoretical massNumber of molelcules
Total (without water)19,1592
Polymers19,1592
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)20 / 60structures with the lowest energy
RepresentativeModel #20minimized average structure

-
Components

#1: Protein PROTEIN KINASE SPK1


Mass: 18148.758 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FHA DOMAIN (FHA2)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: YEAST / Plasmid: PGEX-4T / Production host: Escherichia coli (E. coli)
References: UniProt: P22216, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein/peptide DNA REPAIR PROTEIN RAD9 /


Mass: 1009.947 Da / Num. of mol.: 1 / Fragment: RESIDUES 826-832 / Source method: obtained synthetically / Details: This peptide was synthesized. / References: UniProt: P14737

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

-
Sample preparation

DetailsContents: 0.5 mM FHA2 U-15N,13C; 1 mM phosphotyrosyl peptide of Rad9; 10 mM sodium phosphate buffer (pH 6.5), 1 mM DTT,and 1 mM EDTA
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 10 mM sodium phosphate buffer (pH 6.5), 1 mM DTT,and 1 mM EDTA
pH: 6.5 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 3346 restraints, 3158 distance constraints, and 188 TALOS-derived dihedral angle restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 20

+
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