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- PDB-2jqi: NMR Structure of the Rad53 FHA1 domain in complex with a phosphot... -

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Basic information

Entry
Database: PDB / ID: 2jqi
TitleNMR Structure of the Rad53 FHA1 domain in complex with a phosphothreonien peptide derived from Rad53 SCD1
Components(Serine/threonine-protein kinase RAD53) x 2
KeywordsCELL CYCLE / Protein/phosphopeptide
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / dual-specificity kinase / telomere maintenance in response to DNA damage / DNA replication origin binding / negative regulation of DNA damage checkpoint / 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 / DNA replication origin binding / negative regulation of DNA damage checkpoint / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / protein localization / histone H2AXY142 kinase activity / histone H3Y41 kinase activity / protein kinase activity / protein serine/threonine kinase activity / protein serine kinase activity / DNA repair / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / Serine/threonine-protein kinase, active site ...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 / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsYuan, C. / Mahajan, A. / Tsai, M.
CitationJournal: Mol.Cell / Year: 2008
Title: Diphosphothreonine-specific interaction between an SQ/TQ cluster and an FHA domain in the Rad53-Dun1 kinase cascade.
Authors: Lee, H. / Yuan, C. / Hammet, A. / Mahajan, A. / Chen, E.S. / Wu, M.R. / Su, M.I. / Heierhorst, J. / Tsai, M.D.
History
DepositionJun 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase RAD53
B: Serine/threonine-protein kinase RAD53


Theoretical massNumber of molelcules
Total (without water)18,2912
Polymers18,2912
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 / 100structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 17093.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD53, MEC2, SAD1, SPK1 / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P22216, non-specific serine/threonine protein kinase
#2: Protein/peptide Serine/threonine-protein kinase RAD53 / Serine-protein kinase 1


Mass: 1197.146 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: UniProt: P22216, non-specific serine/threonine protein kinase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-13C NOESY
1213D 13C/15N-filtered (f1), 13C-edited (f3) NOESY
1323D 13C/15N-filtered (f1), 13C-edited (f3) NOESY
1423D 13C-edited (f1), 13C/15N-filtered (f3) NOESY
1512D 13C/15N-filtered (f1,f2) NOESY
1622D 13C/15N-filtered (f1,f2) NOESY
1712D 13C/15N-filtered (f1,f2) TOCSY
1822D 13C/15N-filtered (f1,f2) TOCSY
1922D 13C/15N-filtered (f1,f2) COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N] protein, 0.8 mM peptide, 10 mM sodium phosphate, 1 mM DTT, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-15N] protein, 0.8 mM peptide, 10 mM sodium phosphate, 1 mM DTT, 1 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity_1[U-13C; U-15N]1
0.8 mMentity_21
10 mMsodium phosphate1
1 mMDTT1
1 mMEDTA1
0.5 mMentity_1[U-13C; U-15N]2
0.8 mMentity_22
10 mMsodium phosphate2
1 mMDTT2
1 mMEDTA2
Sample conditionsIonic strength: 10 mM sodium phosphate / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A.T. et al.structure solution
NMRPipeDelaglio, F. et al.processing
NMRViewJohnson, B.A. et al.data analysis
CNS1.1Brunger, A.T. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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