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- PDB-1mv0: NMR STRUCTURE OF THE TUMOR SUPPRESSOR BIN1: ALTERNATIVE SPLICING ... -

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Basic information

Entry
Database: PDB / ID: 1mv0
TitleNMR STRUCTURE OF THE TUMOR SUPPRESSOR BIN1: ALTERNATIVE SPLICING IN MELANOMA AND INTERACTION WITH C-MYC
Components
  • Myc box-dependent-interacting protein 1
  • Myc proto-oncogene protein
KeywordsENDOCYTOSIS/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 / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / lipid tube assembly / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation ...lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / lipid tube assembly / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / T-tubule organization / varicosity / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Regulation of CDH1 mRNA translation by microRNAs / RNA polymerase II transcription repressor complex / cellular response to interferon-alpha / Binding of TCF/LEF:CTNNB1 to target gene promoters / positive regulation of B cell apoptotic process / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of potassium ion transmembrane transport / myotube differentiation / negative regulation of cell division / extrinsic component of synaptic vesicle membrane / negative regulation of monocyte differentiation / positive regulation of astrocyte differentiation / detection of mechanical stimulus involved in sensory perception of sound / aspartic-type endopeptidase inhibitor activity / cerebellar mossy fiber / response to growth factor / axon initial segment / B cell apoptotic process / response to alkaloid / transcription regulator activator activity / node of Ranvier / Transcription of E2F targets under negative control by DREAM complex / RNA polymerase binding / fibroblast apoptotic process / negative regulation of stress-activated MAPK cascade / Regulation of NFE2L2 gene expression / protein-DNA complex disassembly / regulation of neuron differentiation / I band / positive regulation of mesenchymal cell proliferation / regulation of telomere maintenance / skeletal system morphogenesis / Signaling by ALK / branching involved in ureteric bud morphogenesis / middle ear morphogenesis / clathrin binding / endosome to lysosome transport / rRNA metabolic process / nucleus organization / negative regulation of gene expression via chromosomal CpG island methylation / pigmentation / E-box binding / positive regulation of actin filament polymerization / negative regulation of amyloid-beta formation / regulation of heart rate by cardiac conduction / positive regulation of telomere maintenance / skeletal muscle cell differentiation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of endocytosis / chromosome organization / positive regulation of transcription initiation by RNA polymerase II / synaptic vesicle endocytosis / Cyclin E associated events during G1/S transition / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / ERK1 and ERK2 cascade / cytoskeleton organization / T-tubule / axon terminus / positive regulation of epithelial cell proliferation / transcription coregulator binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / G1/S transition of mitotic cell cycle / euchromatin / protein processing / MAPK6/MAPK4 signaling / phospholipid binding / positive regulation of miRNA transcription / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to xenobiotic stimulus / tau protein binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / spindle / endocytosis / Z disc / positive regulation of fibroblast proliferation / Wnt signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / Transcriptional regulation of granulopoiesis / synaptic vesicle / actin filament binding
Similarity search - Function
Amphiphysin 2 / Amphiphysin 2, SH3 domain / Leucine zipper, Myc / Myc leucine zipper domain / Amphiphysin / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / BAR domain ...Amphiphysin 2 / Amphiphysin 2, SH3 domain / Leucine zipper, Myc / Myc leucine zipper domain / Amphiphysin / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / BAR domain / BAR domain profile. / BAR / BAR domain / Helix-loop-helix DNA-binding domain / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / 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 / Myc proto-oncogene protein
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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myc proto-oncogene protein
B: Myc box-dependent-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)10,8362
Polymers10,8362
Non-polymers00
Water00
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/peptide Myc proto-oncogene protein / c-Myc / Transcription factor p64


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


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

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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: 1.4 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
Sample conditionsIonic strength: 0.3 / 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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