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- PDB-1k3n: NMR Structure of the FHA1 Domain of Rad53 in Complex with a Rad9-... -

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Entry
Database: PDB / ID: 1k3n
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 / 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 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 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: 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
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations,structures with the lowest energy
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
Has protein modificationY

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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
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM sodium phosphate, 1mM DTT, and 1 mM EDTA
pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
CNS1Brunger et al.structure solution
CNS1Brunger et al.refinement
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 ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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