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Yorodumi- PDB-1a5e: SOLUTION NMR STRUCTURE OF TUMOR SUPPRESSOR P16INK4A, 18 STRUCTURES -
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-Basic information
Entry | Database: PDB / ID: 1a5e | ||||||
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Title | SOLUTION NMR STRUCTURE OF TUMOR SUPPRESSOR P16INK4A, 18 STRUCTURES | ||||||
Components | TUMOR SUPPRESSOR P16INK4A | ||||||
Keywords | ANTI-ONCOGENE / CELL CYCLE / ANK REPEAT | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Byeon, I.-J.L. / Li, J. / Ericson, K. / Selby, T.L. / Tevelev, A. / Kim, H.-J. / O'Maille, P. / Tsai, M.-D. | ||||||
Citation | 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 1a5e.cif.gz | 804.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a5e.ent.gz | 698 KB | Display | PDB format |
PDBx/mmJSON format | 1a5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/1a5e ftp://data.pdbj.org/pub/pdb/validation_reports/a5/1a5e | HTTPS FTP |
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-Related structure data
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-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16554.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TUMOR SUPPRESSOR P16INK4A / 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | 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 ...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). |
-Sample preparation
Details | Contents: H2O AND D2O |
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Sample conditions | Ionic strength: CA. 0 / pH: 7.5 / Pressure: NO / Temperature: 293 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
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NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE 18 STRUCTURES WERE SUPERIMPOSED IN ORDER TO HAVE BEST FITTING FOR THE BACKBONE ATOMS (N, CA, C) OF RESIDUES 14-134. THE EXPERIMENTAL RESTRAINTS ARE PRESENTED IN ENTRY 1INK.MR. RESIDUES 1- ...Details: THE 18 STRUCTURES WERE SUPERIMPOSED IN ORDER TO HAVE BEST FITTING FOR THE BACKBONE ATOMS (N, CA, C) OF RESIDUES 14-134. THE EXPERIMENTAL RESTRAINTS ARE PRESENTED IN ENTRY 1INK.MR. RESIDUES 1-13 AND 135-156 ARE POORLY DEFINED BY THE EXPERIMENTAL DATA. THUS, NO MEANING SHOULD BE GIVEN TO THOSE RESIDUES' COORDINATES. | ||||||||||||
NMR ensemble | Conformer 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: 18 |