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- PDB-5t2s: Structure of the FHA1 domain of Rad53 bound simultaneously to the... -

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Basic information

Entry
Database: PDB / ID: 5t2s
TitleStructure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and a phosphopeptide.
Components
  • ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP
  • DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53
KeywordsCELL CYCLE / FHA / BRCT / phosphopeptide / protein chimera
Function / homology
Function and homology information


positive regulation of spindle attachment to meiosis I kinetochore / positive regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / positive regulation of DNA replication initiation / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / negative regulation of exit from mitosis / deoxyribonucleoside triphosphate biosynthetic process / Dbf4-dependent protein kinase complex / G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex ...positive regulation of spindle attachment to meiosis I kinetochore / positive regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / positive regulation of DNA replication initiation / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / negative regulation of exit from mitosis / deoxyribonucleoside triphosphate biosynthetic process / Dbf4-dependent protein kinase complex / G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of meiosis I / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / meiotic recombination checkpoint signaling / mitotic DNA replication preinitiation complex assembly / premeiotic DNA replication / Activation of the pre-replicative complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / negative regulation of phosphorylation / Activation of ATR in response to replication stress / protein-containing complex localization / double-strand break repair via break-induced replication / mitotic DNA replication checkpoint signaling / dual-specificity kinase / DNA replication origin binding / negative regulation of DNA damage checkpoint / chromosome, centromeric region / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / protein serine/threonine kinase activator activity / DNA damage checkpoint signaling / chromosome segregation / protein localization / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of protein phosphorylation / phosphorylation / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / chromatin / signal transduction / zinc ion binding / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Regulatory subunit Dfp1/Him1, central region / Dfp1/Him1, central region / Serine/threonine-protein kinase Rad53 / Zinc finger, DBF-type / DBF-type zinc finger superfamily / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / Forkhead associated domain / Forkhead-associated (FHA) domain profile. ...Regulatory subunit Dfp1/Him1, central region / Dfp1/Him1, central region / Serine/threonine-protein kinase Rad53 / Zinc finger, DBF-type / DBF-type zinc finger superfamily / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / 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
Similarity search - Domain/homology
Cell division control protein 7 / Serine/threonine-protein kinase RAD53 / DDK kinase regulatory subunit DBF4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGuarne, A. / Almawi, A. / Matthews, L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-67189 Canada
CitationJournal: Sci Rep / Year: 2016
Title: 'AND' logic gates at work: Crystal structure of Rad53 bound to Dbf4 and Cdc7.
Authors: Almawi, A.W. / Matthews, L.A. / Myrox, P. / Boulton, S. / Lai, C. / Moraes, T. / Melacini, G. / Ghirlando, R. / Duncker, B.P. / Guarne, A.
History
DepositionAug 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Structure summary
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53
B: ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP
C: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53
D: ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,84915
Polymers63,8364
Non-polymers1,01311
Water3,189177
1
A: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53
B: ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1024
Polymers31,9182
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-6 kcal/mol
Surface area15470 Å2
MethodPISA
2
C: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53
D: ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,74711
Polymers31,9182
Non-polymers8299
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-9 kcal/mol
Surface area15110 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-31 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.520, 87.260, 66.150
Angle α, β, γ (deg.)90.00, 94.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 / Dumbbell forming protein 4 / CHEK2 homolog / Serine-protein kinase 1


Mass: 30571.002 Da / Num. of mol.: 2
Fragment: UNP P32325 residues 105-220 linked to UNP P22216 residues 22-162 via LINKER residues VDGS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c
Gene: DBF4, DNA52, YDR052C, D4205, YD9609.07C, RAD53, MEC2, SAD1, SPK1, YPL153C, P2588
Plasmid: modified pET15b
Details (production host): Contains aTEV-removable His6-SUMO tag
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P32325, UniProt: P22216, dual-specificity kinase
#2: Protein/peptide ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP


Mass: 1347.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: short phosphorylated peptide derived from Cdc7 / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06243*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM TRIS pH 8.5 12.5 % PEG 3350 (v/v) / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 4, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→39.674 Å / Num. obs: 36580 / % possible obs: 98.3 % / Redundancy: 2.8 % / CC1/2: 0.99 / Net I/σ(I): 8.15
Reflection shellResolution: 2.2→2.6 Å / Redundancy: 2.8 % / CC1/2: 0.318 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G6G; 3QBZ

1g6g

3qbz


Resolution: 2.4→39.674 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.4
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 1534 5.44 %random
Rwork0.2071 ---
obs0.2083 28179 98.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 66 178 4278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034237
X-RAY DIFFRACTIONf_angle_d0.7335701
X-RAY DIFFRACTIONf_dihedral_angle_d15.0431568
X-RAY DIFFRACTIONf_chiral_restr0.03652
X-RAY DIFFRACTIONf_plane_restr0.002716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.33471470.29252441X-RAY DIFFRACTION99
2.4775-2.5660.29341440.28412404X-RAY DIFFRACTION99
2.566-2.66870.31471400.2672426X-RAY DIFFRACTION99
2.6687-2.79020.26121400.26032438X-RAY DIFFRACTION99
2.7902-2.93720.26671300.24582433X-RAY DIFFRACTION99
2.9372-3.12120.26931530.2252424X-RAY DIFFRACTION99
3.1212-3.3620.25041280.21692424X-RAY DIFFRACTION98
3.362-3.70020.20541480.2032407X-RAY DIFFRACTION97
3.7002-4.23510.20011310.17892405X-RAY DIFFRACTION98
4.2351-5.33370.18211270.15792437X-RAY DIFFRACTION97
5.3337-39.6790.19541460.18762406X-RAY DIFFRACTION95

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