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- PDB-2a5e: SOLUTION NMR STRUCTURE OF TUMOR SUPPRESSOR P16INK4A, RESTRAINED M... -

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Basic information

Entry
Database: PDB / ID: 2a5e
TitleSOLUTION NMR STRUCTURE OF TUMOR SUPPRESSOR P16INK4A, RESTRAINED MINIMIZED MEAN STRUCTURE
ComponentsTUMOR SUPPRESSOR P16INK4A
KeywordsANTI-ONCOGENE / TUMOR-SUPPRESSOR-P16INK4A
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 / Oncogene Induced Senescence / negative regulation of cell growth / 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 / 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. / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Cyclin-dependent kinase inhibitor 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsByeon, I.-J.L. / Li, J. / Ericson, K. / Selby, T.L. / Tevelev, A. / Kim, H.-J. / O'Maille, P. / Tsai, M.-D.
CitationJournal: 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
DepositionFeb 13, 1998Processing site: BNL
Revision 1.0Aug 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
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

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Assembly

Deposited unit
A: TUMOR SUPPRESSOR P16INK4A


Theoretical massNumber of molelcules
Total (without water)16,5551
Polymers16,5551
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)1 / 90CLOSEST TO MEAN STRUCTURE WHICH SHOWS GOOD AGREEMENT WITH THE CONSTRAINTS. NONE OF THE CONSTRAINTS SHOW NOE VIOLATION BIGGER THAN 0.5 A AND DIHEDRAL ANGLE VIOLATION BIGGER THAN 5 DEGREE.
Representative

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Components

#1: Protein TUMOR SUPPRESSOR P16INK4A


Mass: 16554.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P42771

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NMR EXPERIMENTS FOR THE ASSIGNMENTS AND STRUCTURE CALCULATIONS : HN(CA)CB
121HNCA
131CBCA(CO)HN
141HN(CO)CA
151(H)CCH-TOCSY
161HNHA
1713D 15N-EDITED NOESY AND TOCSY
1812D NOESY AND TOCSY
1913D 13C-EDITED NOESY
11013D 15N/13C SIMULTANEOUSLY EDITED NOESY
11114D 15N/13C-EDITED NOESY
11214D 13C/13C-EDITED NOESY.
NMR detailsText: THE SOLUTION STRUCTURE OF THE TUMOR SUPPRESSOR P16INK4A HAS BEEN DETERMINED BY MULTI-DIMENSIONAL HERERONUCLEAR NMR. THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF ...Text: THE SOLUTION STRUCTURE OF THE TUMOR SUPPRESSOR P16INK4A HAS BEEN DETERMINED BY MULTI-DIMENSIONAL HERERONUCLEAR 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 1437 EXPERIMENTAL NMR RESTRAINTS (1370 DISTANCE AND 67 TORSION ANGLE RESTRAINTS).

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Sample preparation

DetailsContents: H2O AND D2O
Sample conditionsIonic strength: CA. 0 / pH: 7.5 / Pressure: NO / 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

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameClassification
X-PLORstructure solution
X-PLORrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: CLOSEST TO MEAN STRUCTURE WHICH SHOWS GOOD AGREEMENT WITH THE CONSTRAINTS. NONE OF THE CONSTRAINTS SHOW NOE VIOLATION BIGGER THAN 0.5 A AND DIHEDRAL ANGLE VIOLATION BIGGER THAN 5 DEGREE.
Conformers calculated total number: 90 / Conformers submitted total number: 1

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