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Yorodumi- PDB-1mv3: NMR STRUCTURE OF THE TUMOR SUPPRESSOR BIN1: ALTERNATIVE SPLICING ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mv3 | ||||||
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Title | NMR STRUCTURE OF THE TUMOR SUPPRESSOR BIN1: ALTERNATIVE SPLICING IN MELANOMA AND INTERACTION WITH C-MYC | ||||||
Components | Myc box dependent interacting protein 1 | ||||||
Keywords | ENDOCYTOSIS/EXOCYTOSIS / TUMOR SUPPRESSOR / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
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 / RNA polymerase II transcription repressor complex / regulation of cell cycle process / T-tubule organization / negative regulation of potassium ion transmembrane transport / varicosity ...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 / RNA polymerase II transcription repressor complex / regulation of cell cycle process / T-tubule organization / negative regulation of potassium ion transmembrane transport / varicosity / extrinsic component of synaptic vesicle membrane / nucleus localization / cerebellar mossy fiber / axon initial segment / positive regulation of astrocyte differentiation / aspartic-type endopeptidase inhibitor activity / node of Ranvier / I band / RNA polymerase binding / regulation of neuron differentiation / clathrin binding / positive regulation of actin filament polymerization / nucleus organization / endosome to lysosome transport / regulation of heart rate by cardiac conduction / negative regulation of amyloid-beta formation / positive regulation of endocytosis / synaptic vesicle endocytosis / axon terminus / cytoskeleton organization / T-tubule / tau protein binding / phospholipid binding / Z disc / endocytosis / actin filament binding / actin cytoskeleton / synaptic vesicle / GTPase binding / Clathrin-mediated endocytosis / nuclear envelope / protein-folding chaperone binding / protease binding / vesicle / endosome / positive regulation of apoptotic process / axon / glutamatergic synapse / dendrite / negative regulation of transcription by RNA polymerase II / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol 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 BIN1(-10,+12A) isoform crystallized by the author contains residues 301-377 and 458- ...SEQUENCE The BIN1(-10,+12A) isoform crystallized by the author contains residues 301-377 and 458-594 of the BIN1 sequence present in the Swiss-Prot reference database (accesion O00499). This isoform is missing residues 378 to 457 of the BIN1 sequence and therefore the BIN1(-10,+12A) sequence matches discontinuously with the reference database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mv3.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1mv3.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 1mv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mv3_validation.pdf.gz | 347.3 KB | Display | wwPDB validaton report |
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Full document | 1mv3_full_validation.pdf.gz | 554.6 KB | Display | |
Data in XML | 1mv3_validation.xml.gz | 92 KB | Display | |
Data in CIF | 1mv3_validation.cif.gz | 113.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/1mv3 ftp://data.pdbj.org/pub/pdb/validation_reports/mv/1mv3 | 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 | Mass: 22470.785 Da / Num. of mol.: 1 / Fragment: isoform BIN1+12A (residues 301-377, 458-594) 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 |
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-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: 1.3 mM Bin1(270-482,+12A) U-15N, 13C, 25 mM sodium phosphate, 150 mM NaCl, 1 mM DTT, 95 % H2O, 5% D2O 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 |