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- PDB-1mv3: NMR STRUCTURE OF THE TUMOR SUPPRESSOR BIN1: ALTERNATIVE SPLICING ... -

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Basic information

Entry
Database: PDB / ID: 1mv3
TitleNMR STRUCTURE OF THE TUMOR SUPPRESSOR BIN1: ALTERNATIVE SPLICING IN MELANOMA AND INTERACTION WITH C-MYC
ComponentsMyc box dependent interacting protein 1
KeywordsENDOCYTOSIS/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 / axon initial segment / cerebellar mossy fiber / positive regulation of astrocyte differentiation / nucleus localization / node of Ranvier / aspartic-type endopeptidase inhibitor activity / I band / RNA polymerase binding / nucleus organization / regulation of neuron differentiation / clathrin binding / positive regulation of actin filament polymerization / endosome to lysosome transport / regulation of heart rate by cardiac conduction / positive regulation of endocytosis / negative regulation of amyloid-beta formation / synaptic vesicle endocytosis / axon terminus / cytoskeleton organization / T-tubule / phospholipid binding / tau protein binding / Z disc / endocytosis / actin filament binding / synaptic vesicle / actin cytoskeleton / GTPase binding / Clathrin-mediated endocytosis / nuclear envelope / protein-folding chaperone binding / protease binding / vesicle / endosome / positive regulation of apoptotic process / axon / dendrite / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Amphiphysin 2 / Amphiphysin 2, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains ...Amphiphysin 2 / Amphiphysin 2, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Myc box-dependent-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPineda-Lucena, A. / Arrowsmith, C.H.
CitationJournal: 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
DepositionSep 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myc box dependent interacting protein 1


Theoretical massNumber of molelcules
Total (without water)22,4711
Polymers22,4711
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 #1lowest energy

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Components

#1: Protein Myc box dependent interacting protein 1 / BIN1 / Bridging integrator 1 / Amphiphysin-like protein / Amphiphysin II / Box-dependent myc- ...BIN1 / Bridging integrator 1 / Amphiphysin-like protein / Amphiphysin II / Box-dependent myc-interacting protein-1


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 3D HETERONUCLEAR NMR TECHNIQUES

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Sample preparation

DetailsContents: 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
Sample conditionsIonic strength: 300e-3 / pH: 6.5 / Pressure: ambient / Temperature: 298 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 UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1DELAGLIO ET AL.processing
DYANA1.5GUNTERT ET AL.structure solution
XEASY1.3.13BARTELS ET AL.data analysis
DYANA1.5GUNTERT ET AL.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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