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- PDB-1j4p: NMR STRUCTURE OF THE FHA1 DOMAIN OF RAD53 IN COMPLEX WITH A RAD9-... -

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Basic information

Entry
Database: PDB / ID: 1j4p
TitleNMR STRUCTURE OF THE FHA1 DOMAIN OF RAD53 IN COMPLEX WITH A RAD9-DERIVED PHOSPHOTHREONINE (AT T155) 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 / G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of DNA strand resection involved in replication fork processing / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / meiotic recombination checkpoint signaling / SUMOylation of transcription factors / negative regulation of phosphorylation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / dual-specificity kinase ...deoxyribonucleoside triphosphate biosynthetic process / G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of DNA strand resection involved in replication fork processing / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / meiotic recombination checkpoint signaling / SUMOylation of transcription factors / negative regulation of phosphorylation / 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 / DNA replication origin binding / negative regulation of DNA damage checkpoint / DNA replication initiation / regulation of DNA repair / enzyme activator activity / 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 / protein serine kinase activity / DNA repair / 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 / THE COMPLEX STRUCTURES ARE GENERATED USING A TOTAL OF 2438 RESTRAINTS. AMONG THEM, 3 ARTIFICAL CONSTRAINTS, 192 TALOS- DERIVED DIHEDRAL ANGLE RESTRAINS, 78 RESTRAINTS FROM H-BOND, 16 INTERMOLECULAR DISTANCE CONSTRAINS, AND 2149 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,7112
Polymers18,7112
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)1 / -
Representative

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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: 1617.754 Da / Num. of mol.: 1 / Fragment: RESIDUES 149-161 / Source method: obtained synthetically
Details: THIS PHOSPHOTHREONINE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
References: UniProt: P14737

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Experimental details

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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.

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Sample preparation

DetailsContents: 0.5 MM FHA1 U-15N,13C 10 MM SODIUM PHOSPHATE BUFFER (PH 6.5), 1MM DTT, AND 1 MM EDTA; 90% H2O, 10% D2O
Sample conditionsIonic strength: 10 mM SODIUM PHOSPHATE, 1mM DTT, AND 1 mM EDTA
pH: 6.50 / Pressure: AMBIENT / Temperature: 293.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionClassification
XwinNMR2.6structure solution
CNS1structure solution
CNS1refinement
RefinementMethod: THE COMPLEX STRUCTURES ARE GENERATED USING A TOTAL OF 2438 RESTRAINTS. AMONG THEM, 3 ARTIFICAL CONSTRAINTS, 192 TALOS- DERIVED DIHEDRAL ANGLE RESTRAINS, 78 RESTRAINTS FROM H-BOND, 16 ...Method: THE COMPLEX STRUCTURES ARE GENERATED USING A TOTAL OF 2438 RESTRAINTS. AMONG THEM, 3 ARTIFICAL CONSTRAINTS, 192 TALOS- DERIVED DIHEDRAL ANGLE RESTRAINS, 78 RESTRAINTS FROM H-BOND, 16 INTERMOLECULAR DISTANCE CONSTRAINS, AND 2149 INTRA-FHA1, INTRA- PEPTIDE DISTANCE CONSTRAINTS.
Software ordinal: 1
NMR ensembleConformers submitted total number: 1

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