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- PDB-1ia8: THE 1.7 A CRYSTAL STRUCTURE OF HUMAN CELL CYCLE CHECKPOINT KINASE CHK1 -

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Basic information

Entry
Database: PDB / ID: 1ia8
TitleTHE 1.7 A CRYSTAL STRUCTURE OF HUMAN CELL CYCLE CHECKPOINT KINASE CHK1
ComponentsCHK1 CHECKPOINT KINASE
KeywordsTRANSFERASE / Protein kinase
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 / negative regulation of mitotic nuclear division / mitotic G2/M transition checkpoint / regulation of mitotic centrosome separation / nucleus organization / inner cell mass cell proliferation / negative regulation of gene expression, epigenetic ...negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / negative regulation of mitotic nuclear division / mitotic G2/M transition checkpoint / regulation of mitotic centrosome separation / nucleus organization / inner cell mass cell proliferation / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination / cellular response to caffeine / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / Activation of ATR in response to replication stress / positive regulation of cell cycle / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / signal transduction in response to DNA damage / replication fork / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / condensed nuclear chromosome / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / TP53 Regulates Transcription of DNA Repair Genes / 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 / intracellular signal transduction / chromatin remodeling / protein domain specific binding / protein phosphorylation / DNA repair / protein serine kinase activity / intracellular membrane-bounded organelle / centrosome / protein serine/threonine kinase activity / apoptotic process / DNA damage response / chromatin / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Checkpoint kinase 1, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 ...Checkpoint kinase 1, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.7 Å
AuthorsChen, P. / Luo, C. / Deng, Y. / Ryan, K. / Register, J. / Margosiak, S. / Tempczyk-Russell, A. / Nguyen, B. / Myers, P. / Lundgren, K. ...Chen, P. / Luo, C. / Deng, Y. / Ryan, K. / Register, J. / Margosiak, S. / Tempczyk-Russell, A. / Nguyen, B. / Myers, P. / Lundgren, K. / Chen Kan, C.-C. / O'Connor, P.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: The 1.7 A crystal structure of human cell cycle checkpoint kinase Chk1: implications for Chk1 regulation.
Authors: Chen, P. / Luo, C. / Deng, Y. / Ryan, K. / Register, J. / Margosiak, S. / Tempczyk-Russell, A. / Nguyen, B. / Myers, P. / Lundgren, K. / Kan, C.C. / O'Connor, P.M.
History
DepositionMar 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHK1 CHECKPOINT KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1392
Polymers33,0431
Non-polymers961
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.2, 65.7, 58.1
Angle α, β, γ (deg.)90, 93.9, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CHK1 CHECKPOINT KINASE


Mass: 33042.988 Da / Num. of mol.: 1 / Fragment: CHK1KD (RESIDUES 1-289)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14757, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 13%PEG8k, 0.15M (NH4)2SO4, 0.1M NaCacodylate, and 2% glycerol., pH 6.8, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 %PEG80001reservoir
20.15 Mammonium sulfate1reservoir
30.1 MNa cacodylate1reservoir
42 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: Osmic confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 35032 / Num. obs: 162012 / % possible obs: 93.68 % / Observed criterion σ(I): 1 / Rsym value: 3.2 / Net I/σ(I): 29.9
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 9 / Num. unique all: 3301 / Rsym value: 18.1 / % possible all: 88.3
Reflection
*PLUS
Num. obs: 35032 / % possible obs: 93.7 % / Num. measured all: 162012 / Rmerge(I) obs: 0.032
Reflection shell
*PLUS
% possible obs: 88.3 % / Rmerge(I) obs: 0.181

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Processing

Software
NameClassification
AMoREphasing
PHASESphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR
Starting model: Cdk2

Resolution: 1.7→7 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Details: CNS AND FRODO WERE ALSO USED DURING REFINEMENT.
RfactorNum. reflectionSelection details
Rfree0.235 -Random
Rwork0.216 --
all-30132 -
Displacement parametersBiso mean: 28.9 Å2
Refinement stepCycle: LAST / Resolution: 1.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 5 181 2370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.3
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d

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