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Yorodumi- PDB-1mv0: NMR STRUCTURE OF THE TUMOR SUPPRESSOR BIN1: ALTERNATIVE SPLICING ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mv0 | ||||||
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Title | NMR STRUCTURE OF THE TUMOR SUPPRESSOR BIN1: ALTERNATIVE SPLICING IN MELANOMA AND INTERACTION WITH C-MYC | ||||||
Components |
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Keywords | ENDOCYTOSIS/EXOCYTOSIS / TRANSCRIPTION / TUMOR SUPPRESSOR/ONCOPROTEIN / TRANSCRIPTION COMPLEX / ENDOCYTOSIS-EXOCYTOSIS | ||||||
Function / homology | Function and homology information lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / lipid tube assembly / SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / RNA polymerase II transcription repressor complex ...lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / lipid tube assembly / SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / RNA polymerase II transcription repressor complex / regulation of cell cycle process / T-tubule organization / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / negative regulation of potassium ion transmembrane transport / RUNX3 regulates WNT signaling / varicosity / TFAP2 (AP-2) family regulates transcription of cell cycle factors / extrinsic component of synaptic vesicle membrane / nucleus localization / negative regulation of cell division / cerebellar mossy fiber / axon initial segment / negative regulation of monocyte differentiation / positive regulation of astrocyte differentiation / aspartic-type endopeptidase inhibitor activity / node of Ranvier / transcription regulator activator activity / Transcription of E2F targets under negative control by DREAM complex / response to growth factor / I band / RNA polymerase binding / regulation of telomere maintenance / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / positive regulation of mesenchymal cell proliferation / protein-DNA complex disassembly / negative regulation of gene expression via chromosomal CpG island methylation / regulation of neuron differentiation / branching involved in ureteric bud morphogenesis / clathrin binding / Signaling by ALK / positive regulation of actin filament polymerization / nucleus organization / endosome to lysosome transport / E-box binding / regulation of heart rate by cardiac conduction / negative regulation of amyloid-beta formation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of endocytosis / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / synaptic vesicle endocytosis / chromosome organization / Cyclin E associated events during G1/S transition / axon terminus / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / : / cytoskeleton organization / T-tubule / ERK1 and ERK2 cascade / transcription coregulator binding / positive regulation of epithelial cell proliferation / response to gamma radiation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / MAPK6/MAPK4 signaling / tau protein binding / NOTCH1 Intracellular Domain Regulates Transcription / phospholipid binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Z disc / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / endocytosis / cellular response to UV / MAPK cascade / positive regulation of fibroblast proliferation / actin filament binding / cellular response to xenobiotic stimulus / actin cytoskeleton / synaptic vesicle / GTPase binding / Clathrin-mediated endocytosis / nuclear envelope / protein-folding chaperone binding / cellular response to hypoxia / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / intracellular iron ion homeostasis / protease binding / Estrogen-dependent gene expression / vesicle / protein dimerization activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Pineda-Lucena, A. / Arrowsmith, C.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: A structure-based model of the c-Myc/Bin1 protein interaction shows alternative splicing of Bin1 and c-Myc phosphorylation are key binding determinants. Authors: Pineda-Lucena, A. / Ho, C.S. / Mao, D.Y. / Sheng, Y. / Laister, R.C. / Muhandiram, R. / Lu, Y. / Seet, B.T. / Katz, S. / Szyperski, T. / Penn, L.Z. / Arrowsmith, C.H. | ||||||
History |
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Remark 999 | SEQUENCE The protein crystallized by the author contains Lys465 which corresponds to Glu576 in the ...SEQUENCE The protein crystallized by the author contains Lys465 which corresponds to Glu576 in the Swiss-Prot entry O00499. This residue conflict is noted in the database reference. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mv0.cif.gz | 586.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mv0.ent.gz | 489.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mv0_validation.pdf.gz | 351.7 KB | Display | wwPDB validaton report |
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Full document | 1mv0_full_validation.pdf.gz | 598.3 KB | Display | |
Data in XML | 1mv0_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 1mv0_validation.cif.gz | 66.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/1mv0 ftp://data.pdbj.org/pub/pdb/validation_reports/mv/1mv0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 1479.724 Da / Num. of mol.: 1 / Fragment: residues 55-68 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P01106 |
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#2: Protein | Mass: 9356.479 Da / Num. of mol.: 1 / Fragment: residues 513-593 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O00499 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: THIS STRUCTURE WAS DETERMINED USING STANDARD 3D HETERONUCLEAR NMR TECHNIQUES |
-Sample preparation
Details | Contents: 1.4 mM Bin1(402-482)/c-Myc(55-68) U-15N, 13C, 25 mM sodium phosphate, 150 mM NaCl, 1 mM DTT, 95% H2O, 5% D2O pH=6.5 Solvent system: 95% H2O/5% D2O |
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Sample conditions | Ionic strength: 300e-3 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |