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- PDB-1bi8: MECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUC... -

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Basic information

Entry
Database: PDB / ID: 1bi8
TitleMECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUCTURES CDK6-P19INK4D INHIBITOR COMPLEX
Components
  • CYCLIN-DEPENDENT KINASE 6
  • CYCLIN-DEPENDENT KINASE INHIBITORCyclin-dependent kinase inhibitor protein
KeywordsCOMPLEX (KINASE/INHIBITOR) / CYCLIN DEPENDENT KINASE / CYCLIN DEPENDENT KINASE INHIBITORY PROTEIN / CDK / INK4 / CELL CYCLE / COMPLEX (KINASE-INHIBITOR) / COMPLEX (KINASE-INHIBITOR) complex
Function / homology
Function and homology information


cyclin D2-CDK6 complex / cyclin D2-CDK4 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 / autophagic cell death / lateral ventricle development / negative regulation of cell cycle G1/S phase transition ...cyclin D2-CDK6 complex / cyclin D2-CDK4 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 / autophagic cell death / lateral ventricle development / negative regulation of cell cycle G1/S phase transition / 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 / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cyclin-dependent protein serine/threonine kinase inhibitor activity / response to vitamin D / gliogenesis / 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 / DNA synthesis involved in DNA repair / 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 / response to UV / response to retinoic acid / Notch signaling pathway / ruffle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / : / sensory perception of sound / response to virus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of erythrocyte differentiation / Oncogene Induced Senescence / G1/S transition of mitotic cell cycle / negative regulation of cell growth / Cyclin D associated events in G1 / negative regulation of epithelial cell proliferation / positive regulation of fibroblast 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 / negative regulation of cell population proliferation / cell division / 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
Cyclin-dependent kinase 6 / Ankyrin repeat-containing domain / Ankyrin repeat / 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 ...Cyclin-dependent kinase 6 / Ankyrin repeat-containing domain / Ankyrin repeat / 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
Cyclin-dependent kinase 4 inhibitor D / Cyclin-dependent kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRusso, A.A. / Tong, L. / Lee, J.O. / Jeffrey, P.D. / Pavletich, N.P.
CitationJournal: Nature / Year: 1998
Title: Structural basis for inhibition of the cyclin-dependent kinase Cdk6 by the tumour suppressor p16INK4a.
Authors: Russo, A.A. / Tong, L. / Lee, J.O. / Jeffrey, P.D. / Pavletich, N.P.
History
DepositionJun 22, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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 INHIBITOR
C: CYCLIN-DEPENDENT KINASE 6
D: CYCLIN-DEPENDENT KINASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)109,4214
Polymers109,4214
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.860, 116.060, 131.490
Angle α, β, γ (deg.)90.00, 110.63, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.965395, 0.252602, 0.064847), (-0.25198, -0.96757, 0.017727), (0.067222, 0.000774, 0.997738)
Vector: 95.66276, 7.52021, -1.44159)

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Components

#1: Protein CYCLIN-DEPENDENT KINASE 6 / / CDK6


Mass: 36987.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SPODOPTERA FRUGIPERDA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HI5
References: UniProt: Q00534, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein CYCLIN-DEPENDENT KINASE INHIBITOR / Cyclin-dependent kinase inhibitor protein / P19INK4D


Mass: 17723.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SPODOPTERA FRUGIPERDA / Production host: Escherichia coli (E. coli) / Strain (production host): HI5 / References: UniProt: P55273

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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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
126 %satammonium sulfate1reservoir
28-12 %dioxane1reservoir
3100 mMMES-Na1reservoir
45 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.006
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1998 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 33400 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 2.65 % / Rsym value: 0.055 / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.32 / % possible all: 91.3
Reflection
*PLUS
Num. measured all: 88741 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 91.3 % / Rmerge(I) obs: 0.32

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BNL-22910

Resolution: 2.8→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: REFINED WITH NCS STRICT THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1407 4.3 %RANDOM
Rwork0.255 ---
obs0.255 27794 85 %-
Displacement parameters
Baniso -1Baniso -3Baniso -2
1--29 Å217.9 Å2-
2----8 Å2
3--37 Å2-
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3397 0 0 0 3397
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.05
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.83.8
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it3.83.8
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: STRICT
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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