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- PDB-1jow: Crystal structure of a complex of human CDK6 and a viral cyclin -

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Basic information

Entry
Database: PDB / ID: 1jow
TitleCrystal structure of a complex of human CDK6 and a viral cyclin
Components
  • CELL DIVISION PROTEIN KINASE 6
  • CYCLIN HOMOLOG
KeywordsCELL CYCLE/TRANSFERASE / CDK-cyclin complex / cyclin fold / CELL CYCLE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


cyclin D2-CDK6 complex / cyclin D3-CDK6 complex / cyclin D1-CDK6 complex / cell dedifferentiation / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Drug-mediated inhibition of CDK4/CDK6 activity / FBXO family protein binding / symbiont-mediated perturbation of host cell cycle progression / lateral ventricle development ...cyclin D2-CDK6 complex / cyclin D3-CDK6 complex / cyclin D1-CDK6 complex / cell dedifferentiation / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Drug-mediated inhibition of CDK4/CDK6 activity / FBXO family protein binding / symbiont-mediated perturbation of host cell cycle progression / lateral ventricle development / negative regulation of myeloid cell differentiation / type B pancreatic cell development / negative regulation of monocyte differentiation / astrocyte development / dentate gyrus development / regulation of cell motility / gliogenesis / Regulation of RUNX1 Expression and Activity / regulation of hematopoietic stem cell differentiation / positive regulation of cell-matrix adhesion / generation of neurons / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of cell cycle / negative regulation of cellular senescence / negative regulation of cell differentiation / negative regulation of osteoblast differentiation / hematopoietic stem cell differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / ruffle / regulation of G2/M transition of mitotic cell cycle / Notch signaling pathway / cyclin binding / regulation of erythrocyte differentiation / Oncogene Induced Senescence / response to virus / G1/S transition of mitotic cell cycle / positive regulation of fibroblast proliferation / negative regulation of epithelial cell proliferation / Cyclin D associated events in G1 / T cell differentiation in thymus / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / regulation of cell cycle / protein phosphorylation / negative regulation of cell population proliferation / cell division / protein serine kinase activity / centrosome / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin domain, herpesvirus / Herpesviridae viral cyclin / Cyclin, herpesvirus / Cyclin-dependent kinase 6 / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal ...Cyclin domain, herpesvirus / Herpesviridae viral cyclin / Cyclin, herpesvirus / Cyclin-dependent kinase 6 / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Cyclin-dependent kinase 6 / Cyclin homolog
Similarity search - Component
Biological speciesSaimiriine herpesvirus 2 (Herpesvirus saimiri)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSchulze-Gahmen, U. / Kim, S.H.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: Structural basis for CDK6 activation by a virus-encoded cyclin.
Authors: Schulze-Gahmen, U. / Kim, S.H.
#1: Journal: To be Published
Title: Crystallization of a Complex between Human CDK6 and a Virus-encoded Cyclin is Critically Dependent on the Addition of Small Charged Organic Molecules
Authors: Schulze-Gahmen, U. / Kim, S.H.
History
DepositionJul 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYCLIN HOMOLOG
B: CELL DIVISION PROTEIN KINASE 6


Theoretical massNumber of molelcules
Total (without water)63,7322
Polymers63,7322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-18 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.140, 70.140, 448.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is the heterodimer in the asymmetric unit

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Components

#1: Protein CYCLIN HOMOLOG / V-CYCLIN


Mass: 28665.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saimiriine herpesvirus 2 (Herpesvirus saimiri)
Genus: Rhadinovirus / Plasmid: pFastBac HTa donor plasmid / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01043
#2: Protein CELL DIVISION PROTEIN KINASE 6 / CDK6 / SERINE/THREONINE-PROTEIN KINASE PLSTIRE


Mass: 35066.332 Da / Num. of mol.: 1 / Fragment: residues 1-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK6 / Plasmid: pFastBac1 donor plasmid / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q00534, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris/HCL, sodium chloride, PEG 3350, calcium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Temperature: 295 K
Details: Schulze-Gahmen, U., (2001) Acta Crystallogr, D57, 1287.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
225 mMTris-HCl1droppH8.0
3150 mM1dropNaCl
410 mMdithiothreitol1drop
50.5 mMEDTA1drop
60.1 Mcalcium acetate1reservoir
710 %PEG33501reservoir
80.15 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 17, 2000
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 12815 / Num. obs: 12783 / % possible obs: 0.98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Rsym value: 0.057 / Net I/σ(I): 29
Reflection shellResolution: 3.1→3.19 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.29 / % possible all: 0.82
Reflection
*PLUS
Num. obs: 12678 / % possible obs: 97.9 % / Num. measured all: 92567 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 81.8 % / Rmerge(I) obs: 0.29

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→19.93 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2293632.74 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.323 959 7.6 %RANDOM
Rwork0.266 ---
all-12629 --
obs-12629 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.9899 Å2 / ksol: 0.272956 e/Å3
Displacement parametersBiso mean: 73.3 Å2
Baniso -1Baniso -2Baniso -3
1-10 Å216.11 Å20 Å2
2--10 Å20 Å2
3----19.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.78 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 0 0 3986
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.451 141 7.8 %
Rwork0.385 1675 -
obs--87.6 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 7.5 % / Rfactor obs: 0.266
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 73.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
LS refinement shell
*PLUS
Rfactor Rfree: 0.451 / % reflection Rfree: 7.8 % / Rfactor Rwork: 0.385

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