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- PDB-1fq1: CRYSTAL STRUCTURE OF KINASE ASSOCIATED PHOSPHATASE (KAP) IN COMPL... -

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Entry
Database: PDB / ID: 1fq1
TitleCRYSTAL STRUCTURE OF KINASE ASSOCIATED PHOSPHATASE (KAP) IN COMPLEX WITH PHOSPHO-CDK2
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN-DEPENDENT KINASE INHIBITOR 3Cyclin-dependent kinase inhibitor protein
KeywordsHydrolase/Transferase / phospho-protein-protein complex / Hydrolase-Transferase COMPLEX
Function / homologyDNA Damage/Telomere Stress Induced Senescence / G2 Phase / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / Protein kinase domain / Activation of the pre-replicative complex / Protein-tyrosine phosphatase-like / CDKN3 domain / Protein kinase, ATP binding site / Protein kinase-like domain superfamily / Orc1 removal from chromatin ...DNA Damage/Telomere Stress Induced Senescence / G2 Phase / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / Protein kinase domain / Activation of the pre-replicative complex / Protein-tyrosine phosphatase-like / CDKN3 domain / Protein kinase, ATP binding site / Protein kinase-like domain superfamily / Orc1 removal from chromatin / Cyclin-dependent kinase inhibitor 3 / Protein kinases ATP-binding region signature. / Serine/threonine-protein kinase, active site / Processing of DNA double-strand break ends / Regulation of TP53 Degradation / Protein-tyrosine phosphatase, catalytic / Protein kinase domain / Tyrosine specific protein phosphatases domain / Regulation of TP53 Activity through Phosphorylation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin-dependent kinase inhibitor 3 (CDKN3) / CDK-mediated phosphorylation and removal of Cdc6 / Cyclin E associated events during G1/S transition / PTK6 Regulates Cell Cycle / Senescence-Associated Secretory Phenotype (SASP) / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of APC/C activators between G1/S and early anaphase / Factors involved in megakaryocyte development and platelet production / Meiotic recombination / Serine/Threonine protein kinases active-site signature. / G0 and Early G1 / Activation of ATR in response to replication stress / Tyrosine specific protein phosphatases family profile. / Cyclin A/B1/B2 associated events during G2/M transition / Protein kinase domain profile. / Cyclin A:Cdk2-associated events at S phase entry / p53-Dependent G1 DNA Damage Response / protein tyrosine/serine/threonine phosphatase activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin A1-CDK2 complex / cyclin E1-CDK2 complex / cyclin E2-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-dependent DNA replication initiation / Y chromosome / cyclin-dependent protein kinase activity / X chromosome / histone phosphorylation / centrosome duplication / centriole replication / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Cajal body / condensed chromosome / cellular response to nitric oxide / cyclin binding / mitotic G1 DNA damage checkpoint / regulation of gene silencing / potassium ion transport / meiotic cell cycle / protein-tyrosine-phosphatase / chromosome, telomeric region / protein tyrosine phosphatase activity / G1/S transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / cell cycle arrest / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Ras protein signal transduction / regulation of G2/M transition of mitotic cell cycle / transcription factor complex / G2/M transition of mitotic cell cycle / regulation of signal transduction by p53 class mediator / DNA replication / endosome / peptidyl-serine phosphorylation / centrosome / cell division / negative regulation of cell population proliferation / DNA repair / protein domain specific binding / protein serine/threonine kinase activity / protein phosphorylation / positive regulation of cell population proliferation / positive regulation of transcription, DNA-templated / negative regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm / Cyclin-dependent kinase 2 / Cyclin-dependent kinase inhibitor 3
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 3 Å resolution
AuthorsSong, H. / Hanlon, N. / Brown, N.R. / Noble, M.E.M. / Johnson, L.N. / Barford, D.
Citation
Journal: Mol.Cell / Year: 2001
Title: Phosphoprotein-protein interactions revealed by the crystal structure of kinase-associated phosphatase in complex with phosphoCDK2.
Authors: Song, H. / Hanlon, N. / Brown, N.R. / Noble, M.E. / Johnson, L.N. / Barford, D.
#1: Journal: Science / Year: 1995
Title: Dephosphorylation of Cdk2 Thr160 by the cyclin dependent kinase-interacting phosphatase KAP in the absence of cyclin
Authors: Poon, R.Y.C. / Hunter, T.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: Cdi1, a human G1 and S phase protein phosphatase that associates with Cdk2
Authors: Gyruris, J. / Golemis, E. / Chertkov, H. / Brent, R.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: The p21Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases
Authors: Harper, J.W. / Adami, G.R. / Wei, N. / Keyomarsi, K. / Elledge, S.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 1, 2000 / Release: May 9, 2001
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 9, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Mar 14, 2018Structure modelDatabase referencesstruct_ref_seq_dif_struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE INHIBITOR 3
B: CELL DIVISION PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4074
Polyers57,8762
Non-polymers5312
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3050
ΔGint (kcal/M)-21
Surface area (Å2)22220
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)134.450, 134.450, 65.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP 32 2 1

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Components

#1: Protein/peptide CYCLIN-DEPENDENT KINASE INHIBITOR 3 / Cyclin-dependent kinase inhibitor protein


Mass: 23819.057 Da / Num. of mol.: 1 / Mutation: C140S / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Description: HOMO SAPIENS / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: Q16667, protein-tyrosine-phosphatase
#2: Protein/peptide CELL DIVISION PROTEIN KINASE 2 /


Mass: 34056.469 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Description: HOMO SAPIENS / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

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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: 2.96 / Density percent sol: 58.52 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000,KCl, Mgacetate,Na cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temp: 4 ℃
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
110 mg/mlprotein1drop
25 mgAMPPNP1drop
350 mMsodium cacodylate1reservoir
48-10 %(w/v)PEG80001reservoir
50.2 M1reservoirKCl
6100 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE BM14 / Synchrotron site: ESRF / Beamline: BM14
DetectorType: ADSC / Detector: CCD / Collection date: Jan 1, 2000
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionB iso Wilson estimate: 95.5 / D resolution high: 3 / D resolution low: 3 / Number obs: 17091 / Observed criterion sigma F: 2 / Observed criterion sigma I: 2 / Rmerge I obs: 0.073 / NetI over sigmaI: 5.6 / Redundancy: 5.3 % / Percent possible obs: 99.7
Reflection shellRmerge I obs: 0.36 / Highest resolution: 3 / Lowest resolution: 3.13 / Redundancy: 5.3 % / Percent possible all: 99.9
Reflection
*PLUS
Number measured all: 89741
Reflection shell
*PLUS
Percent possible obs: 99.6 / MeanI over sigI obs: 1.8

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefineR Free selection details: RANDOM / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.313 / R factor R work: 0.235 / Highest resolution: 3 / Lowest resolution: 2 / Number reflection R free: 702 / Number reflection obs: 13940 / Percent reflection obs: 99.7
Refine hist #LASTHighest resolution: 3 / Lowest resolution: 2
Number of atoms included #LASTProtein: 3822 / Nucleic acid: 0 / Ligand: 32 / Solvent: 0 / Total: 3854
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
Software
*PLUS
Name: CNS / Classification: refinement
Refine
*PLUS
Sigma F: 0
Least-squares process
*PLUS
R factor obs: 0.235 / Highest resolution: 3 / Lowest resolution: 2 / Percent reflection R free: 1
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.8

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