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- PDB-1bi7: MECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUC... -

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Basic information

Entry
Database: PDB / ID: 1bi7
TitleMECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUCTURE OF THE CDK6-P16INK4A TUMOR SUPPRESSOR COMPLEX
Components
  • CYCLIN-DEPENDENT KINASE 6
  • MULTIPLE TUMOR SUPPRESSOR
KeywordsCOMPLEX (KINASE/ANTI-ONCOGENE) / CYCLIN DEPENDENT KINASE / CYCLIN DEPENDENT KINASE INHIBITORY PROTEIN / CDK / INK4 / CELL CYCLE / MULTIPLE TUMOR SUPPRESSOR / MTS1 / COMPLEX (KINASE-ANTI-ONCOGENE) / COMPLEX (KINASE-ANTI-ONCOGENE) complex
Function / homology
Function and homology information


positive regulation of macrophage apoptotic process / senescence-associated heterochromatin focus / cyclin D2-CDK6 complex / cyclin D3-CDK6 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / 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 ...positive regulation of macrophage apoptotic process / senescence-associated heterochromatin focus / cyclin D2-CDK6 complex / cyclin D3-CDK6 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / 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 / negative regulation of mammary gland epithelial cell proliferation / lateral ventricle development / regulation of nucleocytoplasmic transport / positive regulation of smooth muscle cell apoptotic process / negative regulation of myeloid cell differentiation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / type B pancreatic cell development / negative regulation of monocyte differentiation / apoptotic process involved in mammary gland involution / astrocyte development / positive regulation of apoptotic process involved in mammary gland involution / dentate gyrus development / regulation of cell motility / cyclin-dependent protein serine/threonine kinase inhibitor activity / gliogenesis / oncogene-induced cell senescence / Regulation of RUNX1 Expression and Activity / regulation of hematopoietic stem cell differentiation / mammary gland epithelial cell proliferation / positive regulation of cell-matrix adhesion / generation of neurons / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of cell cycle / rRNA transcription / regulation of G1/S transition of mitotic cell cycle / Transcriptional Regulation by VENTX / negative regulation of cellular senescence / replicative senescence / keratinocyte proliferation / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of cell-matrix adhesion / somatic stem cell population maintenance / negative regulation of cell differentiation / hematopoietic stem cell differentiation / NF-kappaB binding / negative regulation of osteoblast differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / cyclin-dependent protein kinase holoenzyme complex / keratinocyte differentiation / regulation of G2/M transition of mitotic cell cycle / ruffle / Notch signaling pathway / cyclin binding / regulation of erythrocyte differentiation / G1/S transition of mitotic cell cycle / negative regulation of cell growth / Oncogene Induced Senescence / response to virus / cellular response to hydrogen peroxide / positive regulation of fibroblast proliferation / negative regulation of epithelial cell proliferation / Cyclin D associated events in G1 / cellular senescence / glucose homeostasis / T cell differentiation in thymus / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Ras protein signal transduction / regulation of cell cycle / negative regulation of cell population proliferation / cell division / protein serine kinase activity / negative regulation of DNA-templated transcription / DNA damage response / centrosome / positive regulation of gene expression / protein kinase binding / nucleolus / negative regulation of transcription by RNA polymerase II / signal transduction / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Cyclin-dependent kinase 6 / Ankyrin repeat-containing domain / : / Ankyrin repeat region circular profile. / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...: / Cyclin-dependent kinase 6 / Ankyrin repeat-containing domain / : / Ankyrin repeat region circular profile. / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 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 inhibitor 2A / Cyclin-dependent kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MAD / Resolution: 3.4 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: MULTIPLE TUMOR SUPPRESSOR


Theoretical massNumber of molelcules
Total (without water)53,5432
Polymers53,5432
Non-polymers00
Water00
1
A: CYCLIN-DEPENDENT KINASE 6
B: MULTIPLE TUMOR SUPPRESSOR

A: CYCLIN-DEPENDENT KINASE 6
B: MULTIPLE TUMOR SUPPRESSOR


Theoretical massNumber of molelcules
Total (without water)107,0864
Polymers107,0864
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566x,-y+1,-z+3/21
Unit cell
Length a, b, c (Å)123.100, 123.100, 112.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein CYCLIN-DEPENDENT KINASE 6 / CDK6


Mass: 36987.328 Da / Num. of mol.: 1
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 MULTIPLE TUMOR SUPPRESSOR / P16INK4A / MTS1


Mass: 16555.586 Da / Num. of mol.: 1
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: P42771

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.08 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 %isopropanol1reservoir
240 mMHEPES-Na1reservoir
35 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorDetector: CCD / Date: Jan 1, 1997 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. obs: 12443 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.068 / Net I/σ(I): 17.7
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 6.9 / Rsym value: 0.33 / % possible all: 96.2
Reflection
*PLUS
Num. measured all: 68633 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 96.2 % / Rmerge(I) obs: 0.33

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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: MIR, MAD / Resolution: 3.4→10 Å / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.33 562 4.8 %RANDOM
Rwork0.227 ---
obs0.227 11109 94.7 %-
Refinement stepCycle: LAST / Resolution: 3.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 0 0 3311
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.94
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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