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- PDB-1d9s: TUMOR SUPPRESSOR P15(INK4B) STRUCTURE BY COMPARATIVE MODELING AND... -

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Basic information

Entry
Database: PDB / ID: 1d9s
TitleTUMOR SUPPRESSOR P15(INK4B) STRUCTURE BY COMPARATIVE MODELING AND NMR DATA
ComponentsCYCLIN-DEPENDENT KINASE 4 INHIBITOR B
KeywordsSIGNALING PROTEIN / HELIX-TURN-HELIX / ANKYRIN REPEAT
Function / homology
Function and homology information


mitotic cell cycle checkpoint signaling / regulation of cell cycle => GO:0051726 / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Cyclin D associated events in G1 / megakaryocyte differentiation / negative regulation of cell cycle G1/S phase transition / : / Oxidative Stress Induced Senescence / cellular response to nutrient ...mitotic cell cycle checkpoint signaling / regulation of cell cycle => GO:0051726 / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Cyclin D associated events in G1 / megakaryocyte differentiation / negative regulation of cell cycle G1/S phase transition / : / Oxidative Stress Induced Senescence / cellular response to nutrient / negative regulation of phosphorylation / cyclin-dependent protein serine/threonine kinase inhibitor activity / negative regulation of glial cell proliferation / negative regulation of G1/S transition of mitotic cell cycle / regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of transforming growth factor beta receptor signaling pathway / spleen development / negative regulation of epithelial cell proliferation / G2/M transition of mitotic cell cycle / cellular senescence / negative regulation of cell population proliferation / protein kinase binding / nucleus / cytoplasm
Similarity search - Function
Domain of unknown function DUF3447 / Ankyrin repeat-containing domain / 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 B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / COMPARATIVE MODELING, RESTRAINT ENERGY MINIMIZATION
Model type detailsminimized average
AuthorsYuan, C. / Ji, L. / Selby, T.L. / Byeon, I.J.L. / Tsai, M.D.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Tumor suppressor INK4: comparisons of conformational properties between p16(INK4A) and p18(INK4C).
Authors: Yuan, C. / Li, J. / Selby, T.L. / Byeon, I.J. / Tsai, M.D.
History
DepositionOct 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2000Provider: 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:
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Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE 4 INHIBITOR B


Theoretical massNumber of molelcules
Total (without water)14,3551
Polymers14,3551
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)10 / 19STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #10minimized average structure

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Components

#1: Protein CYCLIN-DEPENDENT KINASE 4 INHIBITOR B


Mass: 14355.204 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P55271

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
122HNCA
132CBCA(CO)NH
1433D 13C-SEPARATED NOESY
1533D 13C-SEPARATED TOCSY
NMR detailsText: TRIPLE-RESONANCE NMR SPECTROSCOPY WAS USED TO DETERMINE THE P15 STRUCTURE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 MM P15, U-15N; 4 MM HEPES, 1 MM DTT, 5 UM EDTA95% H2O/5% D2O
20.2 MM P15, U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA95% H2O/5% D2O
30.2 MM P15, U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA100% D2O
Sample conditionsIonic strength: 0.1 / 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
XwinNMR2.1BRUKERcollection
X-PLOR3.1BRUNGERrefinement
MODELLER-44SALIstructure solution
RefinementMethod: COMPARATIVE MODELING, RESTRAINT ENERGY MINIMIZATION / Software ordinal: 1
Details: DUE TO THE STRUCTURAL FLEXIBILITY AND INSTABILITY OF P15, ONLY A LIMITED NUMBER OF NMR CONSTRAINTS WERE COLLECTED. BECAUSE P15 SHARES MORE THAN 85% SEQUENCE HOMOLOGY WITH P16, 19 P15 ...Details: DUE TO THE STRUCTURAL FLEXIBILITY AND INSTABILITY OF P15, ONLY A LIMITED NUMBER OF NMR CONSTRAINTS WERE COLLECTED. BECAUSE P15 SHARES MORE THAN 85% SEQUENCE HOMOLOGY WITH P16, 19 P15 STRUCTURES WERE GENERATED BY USING COMPARATIVE MODELING (MODELLER-4) WITH AN ENSEMBLE OF P16(INK4A) NMR STRUCTURES AS TEMPLATES. THE MODELING STRUCTURES WERE THEN SUBJECTED TO 1400 STEPS OF RESTRAINT ENERGY MINIMIZATION (X-PLOR) WITH THE NMR DATA (672 DISTANCE CONSTRAINTS). THE STRUCTURES THAT SATISFY THE NMR CONSTRAINTS WERE PICKED TO REPRESENT P15(INK4B).
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 19 / Conformers submitted total number: 10

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