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- PDB-1hn3: SOLUTION STRUCTURE OF THE N-TERMINAL 37 AMINO ACIDS OF THE MOUSE ... -

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Basic information

Entry
Database: PDB / ID: 1hn3
TitleSOLUTION STRUCTURE OF THE N-TERMINAL 37 AMINO ACIDS OF THE MOUSE ARF TUMOR SUPPRESSOR PROTEIN
ComponentsP19 ARF PROTEIN
KeywordsANTITUMOR PROTEIN / Arf / p19Arf / Tumor Suppressor / p53 / mdm2
Function / homology
Function and homology information


: / senescence-associated heterochromatin focus / : / regulation of cell cycle => GO:0051726 / ubiquitin-protein transferase inhibitor activity / regulation of cell cycle => GO:0051726 / negative regulation of proteolysis involved in protein catabolic process / regulation of protein targeting to mitochondrion / negative regulation of mammary gland epithelial cell proliferation / granular component ...: / senescence-associated heterochromatin focus / : / regulation of cell cycle => GO:0051726 / ubiquitin-protein transferase inhibitor activity / regulation of cell cycle => GO:0051726 / negative regulation of proteolysis involved in protein catabolic process / regulation of protein targeting to mitochondrion / negative regulation of mammary gland epithelial cell proliferation / granular component / negative regulation of hepatocyte proliferation / regulation of apoptotic DNA fragmentation / positive regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of immature T cell proliferation in thymus / : / regulation of nucleocytoplasmic transport / somatic stem cell division / response to xenobiotic stimulus => GO:0009410 / : / autophagy of mitochondrion / positive regulation of protein sumoylation / mitochondrial depolarization / negative regulation of ubiquitin-protein transferase activity / positive regulation of apoptotic process involved in mammary gland involution / negative regulation of phosphorylation / negative regulation of protein neddylation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / regulation of protein export from nucleus / regulation of DNA-binding transcription factor activity / SUMO transferase activity / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / negative regulation of ubiquitin protein ligase activity / negative regulation of cell-matrix adhesion / negative regulation of NF-kappaB transcription factor activity / negative regulation of B cell proliferation / regulation of cyclin-dependent protein serine/threonine kinase activity / apoptotic mitochondrial changes / protein K63-linked ubiquitination / somatic stem cell population maintenance / rRNA transcription / transcription factor binding / negative regulation of cell cycle / NF-kappaB binding / replicative senescence / epidermis development / MDM2/MDM4 family protein binding / negative regulation of ubiquitin-dependent protein catabolic process / response to organonitrogen compound / regulation of G2/M transition of mitotic cell cycle / negative regulation of protein binding / G1/S transition of mitotic cell cycle / negative regulation of protein kinase activity / protein destabilization / regulation of protein stability / negative regulation of cell growth / response to organic cyclic compound / cellular response to hydrogen peroxide / rRNA processing / protein polyubiquitination / positive regulation of protein localization to nucleus / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of cellular senescence / positive regulation of DNA-binding transcription factor activity / disordered domain specific binding / cellular senescence / p53 binding / glucose homeostasis / regulation of gene expression / amyloid fibril formation / protein stabilization / positive regulation of apoptotic process / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / nucleolus / protein kinase binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #60 / Tumor suppressor ARF / Cyclin-dependent kinase inhibitor 2a p19Arf N-terminus / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Tumor suppressor ARF
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / CNS was used for structure calculations
AuthorsDiGiammarino, E.L. / Filippov, I. / Weber, J.D. / Bothner, B. / Kriwacki, R.W.
CitationJournal: Biochemistry / Year: 2001
Title: Solution structure of the p53 regulatory domain of the p19Arf tumor suppressor protein.
Authors: DiGiammarino, E.L. / Filippov, I. / Weber, J.D. / Bothner, B. / Kriwacki, R.W.
History
DepositionDec 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P19 ARF PROTEIN


Theoretical massNumber of molelcules
Total (without water)4,7351
Polymers4,7351
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #11extended conformation

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Components

#1: Protein/peptide P19 ARF PROTEIN


Mass: 4734.634 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-37
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET28A-POLYHIS-SYN-ARF N37 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q64364

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: Backbone dihedral angle restraints were obtained using the program TALOS developed by Cornilescu, G., Delaglio, F. and Bax, A.

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Sample preparation

DetailsContents: 1mM mArfN37 15N or 15N/13C; 10mM potassium phosphate, pH 5.0; 50mM NaCl
Solvent system: 5% D2O; 30% TFE (v/v) in water
Sample conditionsIonic strength: 60 / pH: 5.0 / Pressure: ambient / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1variancollection
NMRPipe1.7Delaglio, F.processing
Felix98MSIdata analysis
CNS1Brunger, A.T.structure solution
CNS1Brunger, A.T.refinement
RefinementMethod: CNS was used for structure calculations / Software ordinal: 1
NMR representativeSelection criteria: extended conformation
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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