[English] 日本語
Yorodumi
- PDB-1j4q: NMR STRUCTURE OF THE FHA1 DOMAIN OF RAD53 IN COMPLEX WITH A RAD9-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j4q
TitleNMR STRUCTURE OF THE FHA1 DOMAIN OF RAD53 IN COMPLEX WITH A RAD9-DERIVED PHOSPHOTHREONINE (AT T192) PEPTIDE
Components
  • DNA REPAIR PROTEIN RAD9
  • PROTEIN KINASE SPK1
KeywordsTRANSFERASE/CELL CYCLE / FHA DOMAIN / RAD53 / RAD9 / PHOSPHOTHREONINE / PHOSPHOPROTEIN / TRANSFERASE-CELL CYCLE COMPLEX
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / negative regulation of DNA strand resection involved in replication fork processing / meiotic recombination checkpoint signaling / SUMOylation of transcription factors / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / dual-specificity kinase / mitotic intra-S DNA damage checkpoint signaling / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding ...deoxyribonucleoside triphosphate biosynthetic process / negative regulation of DNA strand resection involved in replication fork processing / meiotic recombination checkpoint signaling / SUMOylation of transcription factors / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / dual-specificity kinase / mitotic intra-S DNA damage checkpoint signaling / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding / DNA replication initiation / regulation of DNA repair / mitotic G1 DNA damage checkpoint signaling / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / nucleotide-excision repair / enzyme activator activity / intracellular protein localization / double-strand break repair / double-stranded DNA binding / protein tyrosine kinase activity / histone binding / protein kinase activity / regulation of cell cycle / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / chromatin / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytoplasm / cytosol
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 / Aurora kinase / Forkhead associated domain / Forkhead-associated (FHA) domain profile. ...Rad9-like Rad53-binding domain, fungi / Fungal Rad9-like Rad53-binding / Serine/threonine-protein kinase Rad53 / : / : / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Aurora kinase / 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 / THE COMPLEX STRUCTURE ARE GENERATED USING A TOTAL OF 2474 RESTRAINTS. AMONG THEM, 3 ARTIFICIAL CONSTRAINTS, 192 TALOS- DERIVED DIHEDRAL ANGLE RESTRAINTS, 78 H-BOND RESTRAINTS, 22 INTERMOLECULAR DISTANCE CONSTRAINS, AND 2179 INTRA-FHA1, INTRA- PEPTIDE DISTANCE CONSTRAINTS
AuthorsYuan, C. / Yongkiettrakul, S. / Byeon, I.-J.L. / Zhou, S. / Tsai, M.-D.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Solution structures of two FHA1-phosphothreonine peptide complexes provide insight into the structural basis of the ligand specificity of FHA1 from yeast Rad53.
Authors: Yuan, C. / Yongkiettrakul, S. / Byeon, I.J. / Zhou, S. / Tsai, M.D.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Structure of the Fha1 Domain of Yeast Rad53 and Identification of Binding Sites for Both Fha1 and its Target Protein Rad9.
Authors: Liao, H. / Yuan, C. / Su, M.I. / Yongkiettrakul, S. / Qin, D. / Li, H. / Byeon, I.J. / Pei, D. / Tsai, M.D.
History
DepositionOct 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,5832
Polymers18,5832
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)1 / -
Representative

-
Components

#1: Protein PROTEIN KINASE SPK1


Mass: 17093.490 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FHA DOMAIN (FHA1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPK1 OR RAD53 / Plasmid: PGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P22216, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein/peptide DNA REPAIR PROTEIN RAD9


Mass: 1489.474 Da / Num. of mol.: 1 / Fragment: RESIDUES 188-200 / Source method: obtained synthetically
Details: THIS PHOSPHOTHREONINE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
References: UniProt: P14737
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1213D 15N-SEPARATED NOESY
1312D 13C/15N-FILTERED NOESY
1413D 13C -EDITED 13C/15N-FILTERED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY

-
Sample preparation

DetailsContents: 0.5 MM FHA1 U-15N,13C 10 MM SODIUM PHOSPHATE BUFFER (PH 6.5), 1 MM DTT, AND 1 MM EDTA; 90% H2O, 10% D2O
Sample conditionsIonic strength: 10 mM SODIUM PHOSPHATE, 1 mM DTT, AND 1 mM EDTA
pH: 6.5 / Pressure: AMBIENT / Temperature: 293.00 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
NameVersionClassification
XwinNMR2.6structure solution
CNS1structure solution
CNS1refinement
RefinementMethod: THE COMPLEX STRUCTURE ARE GENERATED USING A TOTAL OF 2474 RESTRAINTS. AMONG THEM, 3 ARTIFICIAL CONSTRAINTS, 192 TALOS- DERIVED DIHEDRAL ANGLE RESTRAINTS, 78 H-BOND RESTRAINTS, 22 ...Method: THE COMPLEX STRUCTURE ARE GENERATED USING A TOTAL OF 2474 RESTRAINTS. AMONG THEM, 3 ARTIFICIAL CONSTRAINTS, 192 TALOS- DERIVED DIHEDRAL ANGLE RESTRAINTS, 78 H-BOND RESTRAINTS, 22 INTERMOLECULAR DISTANCE CONSTRAINS, AND 2179 INTRA-FHA1, INTRA- PEPTIDE DISTANCE CONSTRAINTS
Software ordinal: 1
NMR ensembleConformers submitted total number: 1

+
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