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- PDB-1bd8: STRUCTURE OF CDK INHIBITOR P19INK4D -

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Basic information

Entry
Database: PDB / ID: 1bd8
TitleSTRUCTURE OF CDK INHIBITOR P19INK4D
ComponentsP19INK4D CDK4/6 INHIBITOR
KeywordsTUMOR SUPPRESSOR / CDK4/6 INHIBITOR / ANKYRIN MOTIF
Function / homology
Function and homology information


cyclin D2-CDK4 complex / autophagic cell death / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cyclin-dependent protein serine/threonine kinase inhibitor activity / response to vitamin D / DNA synthesis involved in DNA repair / negative regulation of G1/S transition of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / response to retinoic acid / response to UV ...cyclin D2-CDK4 complex / autophagic cell death / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cyclin-dependent protein serine/threonine kinase inhibitor activity / response to vitamin D / DNA synthesis involved in DNA repair / negative regulation of G1/S transition of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / response to retinoic acid / response to UV / sensory perception of sound / negative regulation of cell growth / Oncogene Induced Senescence / Cyclin D associated events in G1 / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / negative regulation of cell population proliferation / protein kinase binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / 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 ...: / 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 / Mainly Alpha
Similarity search - Domain/homology
Cyclin-dependent kinase 4 inhibitor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsBaumgartner, R. / Fernandez-Catalan, C. / Winoto, A. / Huber, R. / Engh, R. / Holak, T.A.
Citation
Journal: Structure / Year: 1998
Title: Structure of human cyclin-dependent kinase inhibitor p19INK4d: comparison to known ankyrin-repeat-containing structures and implications for the dysfunction of tumor suppressor p16INK4a.
Authors: Baumgartner, R. / Fernandez-Catalan, C. / Winoto, A. / Huber, R. / Engh, R.A. / Holak, T.A.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal Structure of the Cdk4/6 Inhibitory Protein P18Ink4C Provides Insights Into Ankyrin-Like Repeat Structure/Function and Tumor-Derived P16Ink4 Mutations
Authors: Venkataramani, R. / Swaminathan, K. / Marmorstein, R.
History
DepositionMay 12, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P19INK4D CDK4/6 INHIBITOR


Theoretical massNumber of molelcules
Total (without water)16,6281
Polymers16,6281
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.470, 54.560, 45.590
Angle α, β, γ (deg.)90.00, 90.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein P19INK4D CDK4/6 INHIBITOR


Mass: 16627.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM / Plasmid: PET-15B / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P55273
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 1.86 Å3/Da / Density % sol: 34 % / Description: DATA COLLECTED IN THE OSCILLATION MODE.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 35% PEG 4000, 200 MM MGSO4 AND 200 MM TRIS/HCL PH 8.5, SITTING DROP METHOD, AT 4 DEG. C., vapor diffusion - sitting drop, temperature 277K
Crystal
*PLUS
Density % sol: 35 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
230 %PEG40001reservoir
30.1 MTris-HCl1reservoir
40.2 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 13017 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.7
Reflection
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameVersionClassification
CCP4SUITEmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Highest resolution: 1.8 Å /
Rfactor% reflection
Rfree0.26 5 %
Rwork0.19 -
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1167 0 0 198 1365
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.0058
X-RAY DIFFRACTIONp_angle_deg0.96

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