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- PDB-7ako: Crystal structure of CHK1 kinase domain in complex with a CLASPIN... -

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Basic information

Entry
Database: PDB / ID: 7ako
TitleCrystal structure of CHK1 kinase domain in complex with a CLASPIN phosphopeptide
Components
  • Claspin
  • Serine/threonine-protein kinase Chk1
KeywordsCELL CYCLE
Function / homology
Function and homology information


DNA secondary structure binding / activation of protein kinase activity / anaphase-promoting complex binding / negative regulation of G0 to G1 transition / apoptotic process involved in development / DNA replication checkpoint signaling / histone H3T11 kinase activity / regulation of mitotic centrosome separation / negative regulation of mitotic nuclear division / mitotic DNA replication checkpoint signaling ...DNA secondary structure binding / activation of protein kinase activity / anaphase-promoting complex binding / negative regulation of G0 to G1 transition / apoptotic process involved in development / DNA replication checkpoint signaling / histone H3T11 kinase activity / regulation of mitotic centrosome separation / negative regulation of mitotic nuclear division / mitotic DNA replication checkpoint signaling / mitotic G2/M transition checkpoint / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / Apoptotic cleavage of cellular proteins / nucleus organization / negative regulation of gene expression, epigenetic / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / peptidyl-threonine phosphorylation / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of ATR in response to replication stress / positive regulation of cell cycle / DNA damage checkpoint signaling / regulation of signal transduction by p53 class mediator / replication fork / condensed nuclear chromosome / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / TP53 Regulates Transcription of DNA Repair Genes / cellular response to mechanical stimulus / Signaling by SCF-KIT / G2/M DNA damage checkpoint / peptidyl-serine phosphorylation / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / Ub-specific processing proteases / chromatin remodeling / protein domain specific binding / protein serine kinase activity / DNA repair / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / apoptotic process / DNA damage response / centrosome / chromatin / Golgi apparatus / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Claspin / Checkpoint kinase 1, catalytic domain / 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
STAUROSPORINE / Serine/threonine-protein kinase Chk1 / Claspin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDay, M. / Oliver, A.W. / Pearl, L.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC302/A24386 United Kingdom
Cancer Research UKC302/A14532 United Kingdom
CitationJournal: Structure / Year: 2021
Title: Structural basis for recruitment of the CHK1 DNA damage kinase by the CLASPIN scaffold protein.
Authors: Day, M. / Parry-Morris, S. / Houghton-Gisby, J. / Oliver, A.W. / Pearl, L.H.
History
DepositionOct 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 31, 2024Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase Chk1
B: Serine/threonine-protein kinase Chk1
C: Claspin
D: Claspin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,94014
Polymers72,5074
Non-polymers1,43310
Water5,657314
1
A: Serine/threonine-protein kinase Chk1
C: Claspin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9727
Polymers36,2532
Non-polymers7185
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-43 kcal/mol
Surface area13650 Å2
MethodPISA
2
B: Serine/threonine-protein kinase Chk1
D: Claspin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9687
Polymers36,2532
Non-polymers7155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-7 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.339, 64.454, 97.082
Angle α, β, γ (deg.)90.000, 96.318, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Serine/threonine-protein kinase Chk1 / CHK1 checkpoint homolog / Cell cycle checkpoint kinase / Checkpoint kinase-1


Mass: 34357.352 Da / Num. of mol.: 2 / Mutation: D10R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK1, CHK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14757, non-specific serine/threonine protein kinase
#2: Protein/peptide Claspin / hClaspin


Mass: 1896.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9HAW4

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Non-polymers , 4 types, 324 molecules

#3: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: antibiotic*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM Sodium citrate tribasic dihydrate, 100 mM Bis-Tris propane pH 6.5 and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 1.8→96.49 Å / Num. obs: 65068 / % possible obs: 96.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 29.03 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 2602 / CC1/2: 0.161

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IA8

1ia8


Resolution: 1.8→96.49 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5014
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2351 2513 4.84 %
Rwork0.19 49434 -
obs0.1922 51947 76.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→96.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 99 314 4970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434782
X-RAY DIFFRACTIONf_angle_d0.72866486
X-RAY DIFFRACTIONf_chiral_restr0.0504692
X-RAY DIFFRACTIONf_plane_restr0.0048819
X-RAY DIFFRACTIONf_dihedral_angle_d21.23991812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.416260.376885X-RAY DIFFRACTION2.4
1.84-1.880.3951220.314418X-RAY DIFFRACTION11.79
1.88-1.920.3156350.303985X-RAY DIFFRACTION27.43
1.92-1.960.3359690.27861638X-RAY DIFFRACTION45.25
1.96-2.010.3317980.27592142X-RAY DIFFRACTION58.7
2.01-2.070.31361360.25622487X-RAY DIFFRACTION70.15
2.07-2.130.30721370.24252815X-RAY DIFFRACTION78.78
2.13-2.20.26431790.23443154X-RAY DIFFRACTION88.06
2.2-2.270.26991750.22693429X-RAY DIFFRACTION95.44
2.27-2.370.26021680.21953573X-RAY DIFFRACTION99.65
2.37-2.470.24442040.22163600X-RAY DIFFRACTION99.66
2.47-2.60.24991670.22783585X-RAY DIFFRACTION99.36
2.6-2.770.29191700.20753612X-RAY DIFFRACTION99.6
2.77-2.980.22851900.20043564X-RAY DIFFRACTION99.29
2.98-3.280.23481790.19283589X-RAY DIFFRACTION99.26
3.28-3.750.22252000.17293583X-RAY DIFFRACTION98.64
3.75-4.730.19661900.13953568X-RAY DIFFRACTION98.2
4.73-96.490.20811880.16553607X-RAY DIFFRACTION96.76

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