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- PDB-2jqj: NMR structure of yeast Dun1 FHA domain -

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Basic information

Entry
Database: PDB / ID: 2jqj
TitleNMR structure of yeast Dun1 FHA domain
ComponentsDNA damage response protein kinase DUN1
KeywordsCELL CYCLE / protein/phosphopeptide
Function / homology
Function and homology information


G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / mitotic DNA damage checkpoint signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / calmodulin-dependent protein kinase activity / DNA damage checkpoint signaling / cellular response to oxidative stress / calmodulin binding / non-specific serine/threonine protein kinase ...G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / mitotic DNA damage checkpoint signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / calmodulin-dependent protein kinase activity / DNA damage checkpoint signaling / cellular response to oxidative stress / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...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 / 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 damage response protein kinase DUN1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsYuan, C. / Lee, H. / Chang, C. / Heierhorst, J. / 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 2, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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_spectrometer.model / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage response protein kinase DUN1


Theoretical massNumber of molelcules
Total (without water)17,3941
Polymers17,3941
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)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein DNA damage response protein kinase DUN1


Mass: 17394.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DUN1 / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P39009, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D TROSY-HN(CA)CB
1213D TROSY-CBCA(CO)NH
1323D HNCA
1423D HN(CO)CA
1533D 1H-13C NOESY
1643D 1H-15N TOCSY
1743D 1H-15N NOESY
1843D HNHA
1943D HNHB
11033D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-13C; U-15N; 60% 2H] protein, 150 mM NaCl, 2 mM DTT, 1 mM EDTA, 5 mM HEPES, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-13C; U-15N] protein, 150 mM NaCl, 1 mM EDTA, 5 mM HEPES, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-13C; U-15N] protein, 150 mM NaCl, 1 mM EDTA, 2 mM DTT, 5 mM HEPES, 100% D2O100% D2O
40.4 mM [U-15N] protein, 150 mM NaCl, 2 mM DTT, 1 mM EDTA, 5 mM HEPES, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMentity[U-13C; U-15N; 60% 2H]1
150 mMNaCl1
2 mMDTT1
1 mMEDTA1
5 mMHEPES1
0.4 mMentity[U-13C; U-15N]2
150 mMNaCl2
1 mMEDTA2
5 mMHEPES2
2 mMDTT2
0.4 mMentity[U-13C; U-15N]3
150 mMNaCl3
1 mMEDTA3
2 mMDTT3
5 mMHEPES3
0.4 mMentity[U-15N]4
150 mMNaCl4
2 mMDTT4
1 mMEDTA4
5 mMHEPES4
Sample conditionsIonic strength: 150 mM NaCl / pH: 7.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE5004

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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 the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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