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- PDB-7akm: Crystal structure of CHK1 kinase domain in complex with ATPyS -

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Basic information

Entry
Database: PDB / ID: 7akm
TitleCrystal structure of CHK1 kinase domain in complex with ATPyS
ComponentsSerine/threonine-protein kinase Chk1
KeywordsCELL CYCLE
Function / homology
Function and homology information


negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / nucleus organization ...negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / nucleus organization / negative regulation of gene expression, epigenetic / cellular response to caffeine / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / 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 / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / condensed nuclear chromosome / replication fork / TP53 Regulates Transcription of DNA Repair Genes / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / peptidyl-threonine phosphorylation / G2/M DNA damage checkpoint / Signaling by SCF-KIT / cellular response to mechanical stimulus / 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 / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein phosphorylation / protein domain specific binding / intracellular membrane-bounded organelle / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA damage response / chromatin / apoptotic process / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / CITRIC ACID / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsDay, M. / Oliver, A.W. / Pearl, L.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC302/A24386 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,77316
Polymers68,4262
Non-polymers1,34714
Water7,819434
1
A: Serine/threonine-protein kinase Chk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0338
Polymers34,2131
Non-polymers8207
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase Chk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7408
Polymers34,2131
Non-polymers5277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.620, 89.270, 112.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 34213.219 Da / Num. of mol.: 2 / Mutation: D10R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK1, CHK1 / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14757, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 448 molecules

#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200 mM Sodium citrate tribasic dihydrate, 100 mM Bis-Tris propane pH 8.5 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: Feb 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 1.93→44.63 Å / Num. obs: 49422 / % possible obs: 98.35 % / Redundancy: 4 % / Biso Wilson estimate: 28.6 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1555 / Rpim(I) all: 0.08786 / Rrim(I) all: 0.1795 / Net I/σ(I): 5.57
Reflection shellResolution: 1.93→1.999 Å / Rmerge(I) obs: 1.313 / Mean I/σ(I) obs: 0.79 / Num. unique obs: 4447 / CC1/2: 0.336 / Rpim(I) all: 0.7813 / Rsym value: 1.54

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Processing

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

1ia8


Resolution: 1.93→44.63 Å / SU ML: 0.2459 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2472
RfactorNum. reflection% reflection
Rfree0.2419 2410 4.88 %
Rwork0.1967 --
obs0.199 49385 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.48 Å2
Refinement stepCycle: LAST / Resolution: 1.93→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 83 434 4891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00394564
X-RAY DIFFRACTIONf_angle_d0.72146174
X-RAY DIFFRACTIONf_chiral_restr0.0473659
X-RAY DIFFRACTIONf_plane_restr0.0035793
X-RAY DIFFRACTIONf_dihedral_angle_d13.8577618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.34981310.33112406X-RAY DIFFRACTION86.85
1.97-2.010.38731410.30912612X-RAY DIFFRACTION94.96
2.01-2.060.31011310.28642700X-RAY DIFFRACTION97.55
2.06-2.110.31451240.26552769X-RAY DIFFRACTION99.38
2.11-2.170.32811410.25372772X-RAY DIFFRACTION99.62
2.17-2.230.26321400.2322771X-RAY DIFFRACTION99.62
2.23-2.30.27271280.20722775X-RAY DIFFRACTION99.73
2.3-2.390.24891430.20512774X-RAY DIFFRACTION99.59
2.39-2.480.26051460.19872786X-RAY DIFFRACTION99.73
2.48-2.590.29461200.20292812X-RAY DIFFRACTION99.73
2.59-2.730.21761410.18792783X-RAY DIFFRACTION99.39
2.73-2.90.26491540.18682779X-RAY DIFFRACTION99.56
2.9-3.130.20841560.18262801X-RAY DIFFRACTION99.66
3.13-3.440.22581530.17852798X-RAY DIFFRACTION99.29
3.44-3.940.20481520.15132824X-RAY DIFFRACTION99.7
3.94-4.960.20221360.15312881X-RAY DIFFRACTION99.6
4.96-44.630.23451730.2262932X-RAY DIFFRACTION98.23

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