- PDB-2jql: NMR structure of the yeast Dun1 FHA domain in complex with a doub... -
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Basic information
Entry
Database: PDB / ID: 2jql
Title
NMR structure of the yeast Dun1 FHA domain in complex with a doubly phosphorylated (pT) peptide derived from Rad53 SCD1
Components
DNA damage response protein kinase DUN1
Serine/threonine-protein kinase RAD53
Keywords
CELL CYCLE / protein/phosphopeptide
Function / homology
Function and homology information
G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / telomere maintenance in response to DNA damage / mitotic DNA damage checkpoint signaling / negative regulation of phosphorylation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / dual-specificity kinase / calcium/calmodulin-dependent protein kinase activity ...G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / telomere maintenance in response to DNA damage / mitotic DNA damage checkpoint signaling / negative regulation of phosphorylation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / dual-specificity kinase / calcium/calmodulin-dependent protein kinase activity / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / 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 / cellular response to oxidative stress / protein tyrosine kinase activity / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function
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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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 / 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
Mass: 1277.126 Da / Num. of mol.: 1 / Source method: obtained synthetically References: UniProt: P22216, non-specific serine/threonine protein kinase
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
2
3D 1H-13C NOESY
1
2
3
3D 1H-15N NOESY
1
3
3
3D HNCA
1
4
3
3DHN(CO)CA
1
5
1
3D 13C/15N-filtered (f1),13C-edited (f3) NOESY
1
6
2
3D 13C/15N-filtered (f1), 13C-edoted (f3) NOESY
1
7
2
3D 13C-edited (f1), 13C/15N-filtered (f3) NOESY
1
8
1
2D 13C/15N-filtered (f1,f2) NOESY
1
9
2
2D 13C/15N-filtered (f1,f2) NOESY
1
10
1
2D 13C/15N-filtered (f1,f2) TOCSY
1
11
1
2D 13C/15N-filtered (f1,f2) TOCSY
1
12
2
2D 13C/15N-filtered (f1,f2) COSY
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
0.4 mM [U-13C; U-15N] protein, 0.5 mM peptide, 5 mM [U-2H] HEPES, 1 mM DTT, 150 mM NaCl, 90% H2O/10% D2O
90% H2O/10% D2O
2
0.4 mM [U-13C; U-15N] protein, 0.5 mM peptide, 5 mM [U-2H] HEPES, 150 mM NaCl, 1 mM DTT, 100% D2O
100% D2O
3
0.4 mM [U-13C; U-15N] protein, 0.5 mM peptide, 5 mM HEPES, 150 mM NaCl, 1 mM EDTA, 2 mM DTT, 90% H2O/10% D2O
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.4mM
entity_1
[U-13C; U-15N]
1
0.5mM
entity_2
1
5mM
HEPES
[U-2H]
1
1mM
DTT
1
150mM
NaCl
1
0.4mM
entity_1
[U-13C; U-15N]
2
0.5mM
entity_2
2
5mM
HEPES
[U-2H]
2
150mM
NaCl
2
1mM
DTT
2
0.4mM
entity_1
[U-13C; U-15N]
3
0.5mM
entity_2
3
5mM
HEPES
3
150mM
NaCl
3
1mM
EDTA
3
2mM
DTT
3
Sample conditions
Ionic strength: 150 mM NaCl / pH: 7.5 / Pressure: ambient / Temperature: 293 K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker Avance
Bruker
AVANCE
800
1
Bruker DMX
Bruker
DMX
600
2
Bruker Avance
Bruker
AVANCE
500
3
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Processing
NMR software
Name
Developer
Classification
NMRPipe
Delaglio, F. etal.
processing
NMRView
Johnson, B.A. etal.
dataanalysis
CNS
Brunger, A.T. etal.
structuresolution
CNS
Brunger, A.T. etal.
refinement
Refinement
Method: simulated annealing / Software ordinal: 1
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20
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