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- PDB-2a0t: NMR structure of the FHA1 domain of Rad53 in complex with a biolo... -

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Basic information

Entry
Database: PDB / ID: 2a0t
TitleNMR structure of the FHA1 domain of Rad53 in complex with a biological relevant phosphopeptide derived from Madt1
Components
  • Hypothetical 73.8 kDa protein in SAS3-SEC17 intergenic region, residues 301-310
  • Serine/threonine-protein kinase RAD53
KeywordsTRANSFERASE / FHA domain. Rad53 / Mdt1 / phosphothreonine / phosphoprotein
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / dual-specificity kinase / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling ...deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / dual-specificity kinase / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / G2/M transition of mitotic cell cycle / intracellular protein localization / protein tyrosine kinase activity / protein kinase activity / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / mRNA binding / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
R3H domain, Cip2-type / Pin4-like, RNA recognition motif / Serine/threonine-protein kinase Rad53 / Tumour Suppressor Smad4 - #20 / : / Tumour Suppressor Smad4 / Aurora kinase / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain ...R3H domain, Cip2-type / Pin4-like, RNA recognition motif / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait 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
Serine/threonine-protein kinase RAD53 / RNA-binding protein PIN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsMahajan, A. / Yuan, C. / Pike, B.L. / Heierhorst, J. / Chang, C.-F. / Tsai, M.-D.
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: FHA Domain-Ligand Interactions: Importance of Integrating Chemical and Biological Approaches
Authors: Mahajan, A. / Yuan, C. / Pike, B.L. / Heierhorst, J. / Chang, C.-F. / Tsai, M.-D.
#1: 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.L. / Zhou, S. / Tsai, M.-D.
History
DepositionJun 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 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:
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Assembly

Deposited unit
A: Serine/threonine-protein kinase RAD53
B: Hypothetical 73.8 kDa protein in SAS3-SEC17 intergenic region, residues 301-310


Theoretical massNumber of molelcules
Total (without water)18,3402
Polymers18,3402
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 acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1closest to the average, lowest energy

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Components

#1: Protein Serine/threonine-protein kinase RAD53 / Serine-protein kinase 1


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, EC: 2.7.1.37
#2: Protein/peptide Hypothetical 73.8 kDa protein in SAS3-SEC17 intergenic region, residues 301-310


Mass: 1246.173 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Saccharomyces cerevisiae (yeast)
References: UniProt: P34217
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-edited 13C/15N-filtered NOESY
1223D 13C/15N-filtered, 13C-edited NOESY
1323D 13C-separated NOESY
1412D 13C/15N-filtered NOESY
1522D 13C/15N-filtered TOCSY
1612D 13C/15N-filtered COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM FHA1 U-13C, 15N, ~0.8 mM peptide, 10 mM sodium phosphate buffer (pH 6.5), 1 mM DTT,1 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
20.5 mM FHA1 U-13C, 15N, ~0.8 mM peptide, 10 mM sodium phosphate buffer (pH 6.5), 1 mM DTT, 1 mM EDTA, 100% D2O100% D2O
Sample conditionsIonic strength: 10 mM sodium phosphate, 1 mM 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002
Bruker AVANCEBrukerAVANCE8003
Bruker AVANCEBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipeDelaglio, F.processing
NMRView5Johnson, B.data analysis
CNS1.1Brunger et al.structure solution
CNS1.1Brunger et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The complex structures are generated using a total of 2524 NMR constraints including constraints in this PDB file and constraints of free FHA1 in PDB access code 1K3J
NMR representativeSelection criteria: closest to the average, lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, 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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