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- PDB-1blx: P19INK4D/CDK6 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1blx
TitleP19INK4D/CDK6 COMPLEX
Components
  • CYCLIN-DEPENDENT KINASE 6
  • P19INK4D
KeywordsCOMPLEX (INHIBITOR PROTEIN/KINASE) / INHIBITOR PROTEIN / CYCLIN-DEPENDENT KINASE / CELL CYCLE CONTROL / ALPHA/BETA / COMPLEX (INHIBITOR PROTEIN-KINASE) / COMPLEX (INHIBITOR PROTEIN-KINASE) complex
Function / homology
Function and homology information


cyclin D2-CDK6 complex / cyclin D2-CDK4 complex / cell dedifferentiation / autophagic cell death / 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 cell cycle G1/S phase transition ...cyclin D2-CDK6 complex / cyclin D2-CDK4 complex / cell dedifferentiation / autophagic cell death / 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 cell cycle G1/S phase transition / negative regulation of myeloid cell differentiation / type B pancreatic cell development / negative regulation of monocyte differentiation / astrocyte development / negative regulation of phosphorylation / dentate gyrus development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / response to vitamin D / 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 / DNA synthesis involved in DNA repair / 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 / cyclin-dependent protein kinase holoenzyme complex / hematopoietic stem cell differentiation / negative regulation of osteoblast differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / response to retinoic acid / response to UV / Notch signaling pathway / ruffle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / response to organic substance / sensory perception of sound / 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
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 6 / Cyclin-dependent kinase 4 inhibitor D
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBrotherton, D.H. / Dhanaraj, V. / Wick, S. / Brizuela, L. / Domaille, P.J. / Volyanik, E. / Xu, X. / Parisini, E. / Smith, B.O. / Archer, S.J. ...Brotherton, D.H. / Dhanaraj, V. / Wick, S. / Brizuela, L. / Domaille, P.J. / Volyanik, E. / Xu, X. / Parisini, E. / Smith, B.O. / Archer, S.J. / Serrano, M. / Brenner, S.L. / Blundell, T.L. / Laue, E.D.
Citation
Journal: Nature / Year: 1998
Title: Crystal structure of the complex of the cyclin D-dependent kinase Cdk6 bound to the cell-cycle inhibitor p19INK4d.
Authors: Brotherton, D.H. / Dhanaraj, V. / Wick, S. / Brizuela, L. / Domaille, P.J. / Volyanik, E. / Xu, X. / Parisini, E. / Smith, B.O. / Archer, S.J. / Serrano, M. / Brenner, S.L. / Blundell, T.L. / Laue, E.D.
#1: Journal: Nature / Year: 1998
Title: Erratum. Crystal Structure of the Complex of the Cyclin D-Dependent Kinase Cdk6 Bound to the Cell-Cycle Inhibitor P19Ink4D
Authors: Brotherton, D.H. / Dhanaraj, V. / Wick, S. / Brizuela, L. / Domaille, P.J. / Volyanik, E. / Xu, X. / Parisini, E. / Smith, B.O. / Archer, S.J. / Serrano, M. / Brenner, S.L. / Blundell, T.L. / Laue, E.D.
History
DepositionJul 21, 1998Processing site: BNL
Revision 1.0Jun 1, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: P19INK4D
A: CALCIUM ION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8603
Polymers54,8202
Non-polymers401
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-15 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.210, 76.410, 93.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYCLIN-DEPENDENT KINASE 6 /


Mass: 36987.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Plasmid: GST FUSION PLASMID / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): BL21 (DE3) / References: UniProt: Q00534
#2: Protein P19INK4D


Mass: 17832.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: SF9 / Plasmid: GST FUSION PLASMID / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q60773
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 %PEG80001reservoir
20.1 MMES1reservoir
30.1 Mcadmium acetate1reservoir

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9475
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 1, 1998 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9475 Å / Relative weight: 1
ReflectionResolution: 1.9→18.54 Å / Num. obs: 41965 / % possible obs: 98.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 8.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.327 / % possible all: 97.7
Reflection
*PLUS
Num. measured all: 166218

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1HCK AND 1AP7

1hck

1ap7


Resolution: 1.9→18.54 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.253 -5 %
Rwork0.2 --
obs-41965 98.5 %
Refinement stepCycle: LAST / Resolution: 1.9→18.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 1 294 3860
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.024
X-RAY DIFFRACTIONp_angle_deg2.3

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