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- PDB-1g3n: STRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1g3n
TitleSTRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX
Components
  • CYCLIN-DEPENDENT KINASE 6 INHIBITOR
  • CYCLIN-DEPENDENT KINASE 6
  • V-CYCLIN
Keywordscell cycle / signaling protein / Cyclin-dependent kinase / INK4 inhibitor / Viral cyclin
Function / homology
Function and homology information


cyclin D2-CDK6 complex / cell dedifferentiation / Drug-mediated inhibition of CDK4/CDK6 activity / 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 / FBXO family protein binding / lateral ventricle development / negative regulation of myeloid cell differentiation / type B pancreatic cell development / negative regulation of monocyte differentiation ...cyclin D2-CDK6 complex / cell dedifferentiation / Drug-mediated inhibition of CDK4/CDK6 activity / 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 / FBXO family protein binding / lateral ventricle development / negative regulation of myeloid cell differentiation / type B pancreatic cell development / negative regulation of monocyte differentiation / astrocyte development / dentate gyrus development / negative regulation of phosphorylation / gliogenesis / cyclin-dependent protein serine/threonine kinase inhibitor activity / regulation of cell motility / Regulation of RUNX1 Expression and Activity / regulation of hematopoietic stem cell differentiation / positive regulation of cell-matrix adhesion / generation of neurons / oligodendrocyte differentiation / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of cellular senescence / negative regulation of cell differentiation / negative regulation of cell cycle / hematopoietic stem cell differentiation / cyclin-dependent protein kinase holoenzyme complex / negative regulation of osteoblast differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / negative regulation of stem cell proliferation / Notch signaling pathway / ruffle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / response to organic substance / stem cell proliferation / G1/S transition of mitotic cell cycle / response to virus / regulation of erythrocyte differentiation / Oncogene Induced Senescence / negative regulation of cell growth / Cyclin D associated events in G1 / positive regulation of fibroblast proliferation / negative regulation of epithelial cell proliferation / T cell differentiation in thymus / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / regulation of cell cycle / cell cycle / cell division / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / centrosome / positive regulation of gene expression / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
K cyclin, C-terminal / K cyclin, C terminal / Cyclin D / Cyclin, herpesvirus / Cyclin-dependent kinase 6 / Cyclins signature. / Cyclin / Cyclin-like / Ankyrin repeat-containing domain / Cyclin A; domain 1 ...K cyclin, C-terminal / K cyclin, C terminal / Cyclin D / Cyclin, herpesvirus / Cyclin-dependent kinase 6 / Cyclins signature. / Cyclin / Cyclin-like / Ankyrin repeat-containing domain / Cyclin A; domain 1 / Ankyrin repeats (many copies) / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 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
V-cyclin / Cyclin-dependent kinase 4 inhibitor C / Cyclin-dependent kinase 6 / Kaposi's sarcoma-associated herpesvirus cyclin homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 8
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJeffrey, P.D. / Tong, L. / Pavletich, N.P.
CitationJournal: Genes Dev. / Year: 2000
Title: Structural basis of inhibition of CDK-cyclin complexes by INK4 inhibitors.
Authors: Jeffrey, P.D. / Tong, L. / Pavletich, N.P.
History
DepositionOct 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE 6
B: CYCLIN-DEPENDENT KINASE 6 INHIBITOR
C: V-CYCLIN
E: CYCLIN-DEPENDENT KINASE 6
F: CYCLIN-DEPENDENT KINASE 6 INHIBITOR
G: V-CYCLIN


Theoretical massNumber of molelcules
Total (without water)166,4626
Polymers166,4626
Non-polymers00
Water0
1
A: CYCLIN-DEPENDENT KINASE 6
B: CYCLIN-DEPENDENT KINASE 6 INHIBITOR
C: V-CYCLIN


Theoretical massNumber of molelcules
Total (without water)83,2313
Polymers83,2313
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: CYCLIN-DEPENDENT KINASE 6
F: CYCLIN-DEPENDENT KINASE 6 INHIBITOR
G: V-CYCLIN


Theoretical massNumber of molelcules
Total (without water)83,2313
Polymers83,2313
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-17 kcal/mol
Surface area29470 Å2
MethodPISA
3
A: CYCLIN-DEPENDENT KINASE 6
C: V-CYCLIN
E: CYCLIN-DEPENDENT KINASE 6
G: V-CYCLIN


Theoretical massNumber of molelcules
Total (without water)130,1634
Polymers130,1634
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-39 kcal/mol
Surface area44560 Å2
MethodPISA
4
A: CYCLIN-DEPENDENT KINASE 6
B: CYCLIN-DEPENDENT KINASE 6 INHIBITOR
E: CYCLIN-DEPENDENT KINASE 6
F: CYCLIN-DEPENDENT KINASE 6 INHIBITOR


Theoretical massNumber of molelcules
Total (without water)110,2734
Polymers110,2734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-18 kcal/mol
Surface area39050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.780, 146.950, 164.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein CYCLIN-DEPENDENT KINASE 6 / / E.C.2.7.1.37 / CELL DIVISION PROTEIN KINASE 6 / PROTEIN KINASE CDK6


Mass: 36987.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYCLIN-DEPENDENT KINASE 6 / Production host: unidentified baculovirus / Strain (production host): HI5 / References: UniProt: Q00534, EC: 2.7.1.37
#2: Protein CYCLIN-DEPENDENT KINASE 6 INHIBITOR / P18(INK4C) / CYCLIN-DEPENDENT KINASE INHIBITOR 2C / P18 / INHIBITS CDK4 / CYCLIN-DEPENDENT KINASE 4 ...P18(INK4C) / CYCLIN-DEPENDENT KINASE INHIBITOR 2C / P18 / INHIBITS CDK4 / CYCLIN-DEPENDENT KINASE 4 INHIBITOR C / P18-INK4C


Mass: 18149.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P18(INK4C) / Production host: Escherichia coli (E. coli) / References: UniProt: P42773
#3: Protein V-CYCLIN / K-CYCLIN / FUNCTIONAL CYCLIN D HOMOLOG


Mass: 28094.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Genus: Rhadinovirus / Gene: K-CYCLIN (VIRAL CYCLIND HOMOLOG) / Production host: Escherichia coli (E. coli) / References: UniProt: O40946, UniProt: Q98147*PLUS

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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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: (NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mM1dropNaCl
25 mMdithiothreitol1drop
35 mM1dropMgCl2
40.5 mMATP1drop
525 mMTris-Cl1drop
61.0 mg/mlprotein1drop
738 %satammonium sulfate1reservoir
86 %(v/v)dioxane1reservoir
95 mMdithiothreitol1reservoir
10100 mMTris-Cl1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 20, 1999 / Details: Mirrors
RadiationMonochromator: Mirror, Yale Design / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. all: 40272 / Num. obs: 40272 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.299 / % possible all: 91.9
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 131920
Reflection shell
*PLUS
% possible obs: 91.9 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1905 5 %Random
Rwork0.224 ---
all0.242 35729 --
obs0.228 33824 --
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10652 0 0 0 10652
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.76
X-RAY DIFFRACTIONc_bond_d0.013
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 15 Å / σ(F): 1 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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