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- PDB-1dc2: SOLUTION NMR STRUCTURE OF TUMOR SUPPRESSOR P16INK4A, 20 STRUCTURES -

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Entry
Database: PDB / ID: 1dc2
TitleSOLUTION NMR STRUCTURE OF TUMOR SUPPRESSOR P16INK4A, 20 STRUCTURES
ComponentsCYCLIN-DEPENDENT KINASE 4 INHIBITOR A (P16INK4A)
KeywordsGENE REGULATION / ANKYRIN REPEAT / HELIX-TURN-HELIX / HELIX BUNDLE
Function / homology
Function and homology information


senescence-associated heterochromatin focus / positive regulation of macrophage apoptotic process / 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 / 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 smooth muscle cell apoptotic process / negative regulation of phosphorylation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity ...senescence-associated heterochromatin focus / positive regulation of macrophage apoptotic process / 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 / 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 smooth muscle cell apoptotic process / negative regulation of phosphorylation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / negative regulation of cell-matrix adhesion / negative regulation of NF-kappaB transcription factor activity / regulation of G1/S transition of mitotic cell cycle / Transcriptional Regulation by VENTX / replicative senescence / NF-kappaB binding / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / negative regulation of cell growth / Oncogene Induced Senescence / Cyclin D associated events in G1 / cellular senescence / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Ras protein signal transduction / regulation of cell cycle / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / protein kinase binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ankyrin repeat-containing domain / Ankyrin repeat region circular profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Cyclin-dependent kinase inhibitor 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsByeon, I.-J.L. / Li, J. / Yuan, C. / Tsai, M.-D.
Citation
Journal: Protein Sci. / Year: 2000
Title: Tumor suppressor INK4: refinement of p16INK4A structure and determination of p15INK4B structure by comparative modeling and NMR data.
Authors: Yuan, C. / Selby, T.L. / Li, J. / Byeon, I.J. / Tsai, M.D.
#1: Journal: Mol.Cell / Year: 1998
Title: Tumor Suppressor p16INK4A: Determination of Solution Structure and Analyses of Its Interaction with Cyclin-Dependent Kinase 4
Authors: Byeon, I.-J. / Li, J. / Ericson, K. / Selby, T.L. / Tevelev, A. / Kim, H.J. / O'Maille, P. / Tsai, M.-D.
History
DepositionNov 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE 4 INHIBITOR A (P16INK4A)


Theoretical massNumber of molelcules
Total (without water)16,5551
Polymers16,5551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60THE CLOSEST TO MEAN STRUCTURE WHICH SHOWS GOOD AGREEMENT WITH THE EXPERIMENTAL RESTRAINTS
RepresentativeModel #20minimized average structure

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Components

#1: Protein CYCLIN-DEPENDENT KINASE 4 INHIBITOR A (P16INK4A)


Mass: 16554.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PTG / Production host: Escherichia coli (E. coli) / References: UniProt: P42771

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1214D 13C-SEPARATED NOESY
1314D 13C/15N-SEPARATED NOESY
1423D 15N-SEPARATED NOESY
152HNHA
1632D NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY.

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Sample preparation

Details
Solution-IDContents
10.2-0.4 MM P16INK4A U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA; 95% H2O, 5% D2O
20.2-0.4 MM P16INK4A U-15N; 4 MM HEPES, 1 MM DTT, 5 UM EDTA; 95% H2O, 5% D2O
30.2-0.4 MM P16INK4A; 4 MM HEPES, 1 MM DTT, 5 UM EDTA; 95% H2O, 5% D2O
Sample conditionsIonic strength: 0 / pH: 7.5 / Pressure: AMBIENT / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.85BRUNGERstructure solution
XwinNMR2.1BRUKERcollection
Felix95MOLECULAR SIMULATIONS INC.processing
XwinNMR2.1BRUKERprocessing
X-PLOR3.85BRUNGERrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1439 RESTRAINTS, 1372 DISTANCE RESTRAINTS, 67 TORSION ANGLE RESTRAINTS.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: THE CLOSEST TO MEAN STRUCTURE WHICH SHOWS GOOD AGREEMENT WITH THE EXPERIMENTAL RESTRAINTS
Conformers calculated total number: 60 / Conformers submitted total number: 20

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