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- PDB-1fin: CYCLIN A-CYCLIN-DEPENDENT KINASE 2 COMPLEX -

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Entry
Database: PDB / ID: 1fin
TitleCYCLIN A-CYCLIN-DEPENDENT KINASE 2 COMPLEX
Components
  • CYCLIN A
  • CYCLIN-DEPENDENT KINASE 2
KeywordsCOMPLEX (TRANSFERASE/CYCLIN) / COMPLEX (TRANSFERASE-CYCLIN) / CYCLIN / CDK / PHOSPHORYLATION / COMPLEX (TRANSFERASE-CYCLIN) complex
Function / homologyTranscription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / Protein kinase-like domain superfamily / Senescence-Associated Secretory Phenotype (SASP) / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of APC/C activators between G1/S and early anaphase / Activation of ATR in response to replication stress / Cyclin-like / Protein kinase, ATP binding site / Cdc20:Phospho-APC/C mediated degradation of Cyclin A ...Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / Protein kinase-like domain superfamily / Senescence-Associated Secretory Phenotype (SASP) / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of APC/C activators between G1/S and early anaphase / Activation of ATR in response to replication stress / Cyclin-like / Protein kinase, ATP binding site / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / G0 and Early G1 / Ub-specific processing proteases / Cyclin-A, N-terminal / Protein kinase domain profile. / Cyclin-like superfamily / Cyclin / Cyclins signature. / Serine/Threonine protein kinases active-site signature. / Protein kinases ATP-binding region signature. / N-terminal region of cyclin_N / Cyclin, C-terminal domain / DNA Damage/Telomere Stress Induced Senescence / Processing of DNA double-strand break ends / Protein kinase domain / Cyclin, C-terminal domain / Factors involved in megakaryocyte development and platelet production / Meiotic recombination / PTK6 Regulates Cell Cycle / Cyclin A:Cdk2-associated events at S phase entry / p53-Dependent G1 DNA Damage Response / Protein kinase domain / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin E associated events during G1/S transition / Cyclin, N-terminal / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Serine/threonine-protein kinase, active site / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / CDK-mediated phosphorylation and removal of Cdc6 / Activation of the pre-replicative complex / Orc1 removal from chromatin / G2 Phase / Regulation of TP53 Degradation / Regulation of TP53 Activity through Phosphorylation / Cyclin, N-terminal domain / cellular response to luteinizing hormone stimulus / cellular response to cocaine / cell cycle G1/S phase transition / male pronucleus / female pronucleus / cellular response to insulin-like growth factor stimulus / cellular response to leptin stimulus / cochlea development / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to platelet-derived growth factor stimulus / regulation of DNA replication / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of mitotic nuclear division / cyclin E1-CDK2 complex / cyclin E2-CDK2 complex / cyclin A1-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 / positive regulation of cell cycle / regulation of gene silencing / potassium ion transport / meiotic cell cycle / cellular response to estradiol stimulus / chromosome, telomeric region / animal organ regeneration / G1/S transition of mitotic cell cycle / positive regulation of fibroblast proliferation / anaphase-promoting complex-dependent catabolic process / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Ras protein signal transduction / cellular response to hypoxia / regulation of G2/M transition of mitotic cell cycle / 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 / protein deubiquitination / centrosome
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2.3 Å resolution
AuthorsJeffrey, P.D. / Russo, A.A. / Pavletich, N.P.
CitationJournal: Nature / Year: 1995
Title: Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex.
Authors: Jeffrey, P.D. / Russo, A.A. / Polyak, K. / Gibbs, E. / Hurwitz, J. / Massague, J. / Pavletich, N.P.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 14, 1996 / Release: Jan 27, 1997
RevisionDateData content typeGroupProviderType
1.0Jan 27, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE 2
B: CYCLIN A
C: CYCLIN-DEPENDENT KINASE 2
D: CYCLIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7026
Polyers127,6884
Non-polymers1,0142
Water7,494416
1
A: CYCLIN-DEPENDENT KINASE 2
B: CYCLIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3513
Polyers63,8442
Non-polymers5071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4170
ΔGint (kcal/M)-15
Surface area (Å2)22830
MethodPISA
2
C: CYCLIN-DEPENDENT KINASE 2
D: CYCLIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3513
Polyers63,8442
Non-polymers5071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4050
ΔGint (kcal/M)-12
Surface area (Å2)22760
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)185.100, 185.100, 214.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP 62 2 2

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Components

#1: Protein/peptide CYCLIN-DEPENDENT KINASE 2 / / CDK2


Mass: 33976.488 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Cell line: SF9 / Plasmid name: PET3A / Genus (production host): Spodoptera / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P24941, Transferases, Transferring phosphorus-containing groups, Phosphotransferases with an alcohol group as acceptor
#2: Protein/peptide CYCLIN A /


Mass: 29867.512 Da / Num. of mol.: 2 / Fragment: RESIDUES 173 - 432 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo
Description: THE FRAGMENT USED IN THE CRYSTALLIZATION WAS PRODUCED BY THE CLEAVAGE OF FULL-LENGTH CYCLIN A BY SUBTILISIN
Cell line: SF9 / Plasmid name: PET3A / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / Strain (production host): SF9 / References: UniProt: P20248
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.16 / Density percent sol: 7 %
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
125 mg/mlCDK2 and cyclinA fragment1drop
240 mMHEPES1drop
30.2 M1dropNaCl
45 mMDTT1drop
528 %satammonium sulfate1reservoir
61 M1reservoirKCl
740 mMHEPES1reservoir
85 mMDTT1reservoir
910 mMATP1reservoir

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Data collection

SourceSource: SYNCHROTRON / Type: CHESS BEAMLINE A1 / Synchrotron site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorDetector: CCD / Collection date: Feb 10, 1995
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 / Relative weight: 1
ReflectionNumber obs: 86466 / Rmerge I obs: 0.061 / Redundancy: 7.8 % / Percent possible obs: 90.2
Reflection
*PLUS
D resolution high: 2.3 / Number measured all: 677413

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Processing

Software
NameClassification
TNTrefinement
HKLdata reduction
RefineSigma F: 2
Least-squares processR factor R work: 0.208 / Highest resolution: 2.3 / Lowest resolution: 6 / Number reflection obs: 70208 / Percent reflection obs: 90.2
Refine hist #LASTHighest resolution: 2.3 / Lowest resolution: 6
Number of atoms included #LASTProtein: 8998 / Nucleic acid: 0 / Ligand: 62 / Solvent: 416 / Total: 9476
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg1.77
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.208

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