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- PDB-1bu9: SOLUTION STRUCTURE OF P18-INK4C, 21 STRUCTURES -

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Entry
Database: PDB / ID: 1bu9
TitleSOLUTION STRUCTURE OF P18-INK4C, 21 STRUCTURES
ComponentsPROTEIN (CYCLIN-DEPENDENT KINASE 6 INHIBITOR)
KeywordsHORMONE/GROWTH FACTOR / CELL CYCLE INHIBITOR / P18INK4C / TUMOR / SUPPRESSOR / CYCLIN-DEPENDENT KINASE / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


negative regulation of phosphorylation / cyclin-dependent protein serine/threonine kinase inhibitor activity / regulation of cyclin-dependent protein serine/threonine kinase activity / oligodendrocyte differentiation / regulation of G1/S transition of mitotic cell cycle / negative regulation of stem cell proliferation / stem cell proliferation / negative regulation of cell growth / Oncogene Induced Senescence / Cyclin D associated events in G1 ...negative regulation of phosphorylation / cyclin-dependent protein serine/threonine kinase inhibitor activity / regulation of cyclin-dependent protein serine/threonine kinase activity / oligodendrocyte differentiation / regulation of G1/S transition of mitotic cell cycle / negative regulation of stem cell proliferation / stem cell proliferation / 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 / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ankyrin repeats (many copies) / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily ...: / Ankyrin repeats (many copies) / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Cyclin-dependent kinase 4 inhibitor C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsByeon, I.-J.L. / Li, J. / Tsai, M.-D.
CitationJournal: Biochemistry / Year: 1999
Title: Tumor suppressor INK4: determination of the solution structure of p18INK4C and demonstration of the functional significance of loops in p18INK4C and p16INK4A.
Authors: Li, J. / Byeon, I.J. / Ericson, K. / Poi, M.J. / O'Maille, P. / Selby, T. / Tsai, M.D.
History
DepositionSep 15, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 13, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: 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: PROTEIN (CYCLIN-DEPENDENT KINASE 6 INHIBITOR)


Theoretical massNumber of molelcules
Total (without water)18,1491
Polymers18,1491
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)21 / 50CLOSEST TO MEAN STRUCTURE WHICH SHOWS GOOD AGREEMENT WITH THE CONSTRAINTS
Representative

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Components

#1: Protein PROTEIN (CYCLIN-DEPENDENT KINASE 6 INHIBITOR) / P18-INK4C


Mass: 18149.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: DL21(DE3) / Production host: Escherichia coli (E. coli) / Strain (production host): DL21(DE3) / References: UniProt: P42773

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB
121HNCA
131CBCA(CO)HN
141HN(CO)(H)CCH-TOCSY
151HNHB
1613D 15N-EDITED NOESY AND TOCSY
1712D NOESY AND TOCSY
1813D 13C-EDITED NOESY
1913D 15N/13C SA EDITED NOESY
11014D 15N/13C-EDITED NOESY
11114D 13C/13C-EDITED NOES
NMR detailsText: THE SOLUTION STRUCTURE OF P18-INK4C HAS BEEN DETERMINED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR. THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) ...Text: THE SOLUTION STRUCTURE OF P18-INK4C HAS BEEN DETERMINED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR. THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER). THE CALCULATION IS BASED ON 3175 EXPERIMENTAL NMR RESTRAINTS (3062 DISTANCE AND 113 TORSION ANGLE RESTRAINTS).

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Sample preparation

Sample conditionspH: 7.5 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX600BrukerDMX6006001
Bruker DRX800BrukerDRX8008002

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: CLOSEST TO MEAN STRUCTURE WHICH SHOWS GOOD AGREEMENT WITH THE CONSTRAINTS
Conformers calculated total number: 50 / Conformers submitted total number: 21

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