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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


negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / 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 / lipid tube assembly / SCF ubiquitin ligase complex binding / Myc-Max complex / negative regulation of transcription initiation by RNA polymerase II / nucleus localization ...negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / 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 / lipid tube assembly / SCF ubiquitin ligase complex binding / Myc-Max complex / negative regulation of transcription initiation by RNA polymerase II / nucleus localization / varicosity / T-tubule organization / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / RNA polymerase II transcription repressor complex / RUNX3 regulates WNT signaling / negative regulation of potassium ion transmembrane transport / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of cell division / extrinsic component of synaptic vesicle membrane / negative regulation of monocyte differentiation / cerebellar mossy fiber / positive regulation of astrocyte differentiation / aspartic-type endopeptidase inhibitor activity / response to growth factor / axon initial segment / transcription regulator activator activity / node of Ranvier / protein-DNA complex disassembly / Transcription of E2F targets under negative control by DREAM complex / RNA polymerase binding / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / I band / Regulation of NFE2L2 gene expression / regulation of telomere maintenance / regulation of neuron differentiation / positive regulation of mesenchymal cell proliferation / clathrin binding / Signaling by ALK / branching involved in ureteric bud morphogenesis / positive regulation of actin filament polymerization / negative regulation of gene expression via chromosomal CpG island methylation / endosome to lysosome transport / rRNA metabolic process / nucleus organization / E-box binding / negative regulation of amyloid-beta formation / positive regulation of telomere maintenance / positive regulation of endocytosis / regulation of heart rate by cardiac conduction / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / synaptic vesicle endocytosis / chromosome organization / core promoter sequence-specific DNA binding / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / signaling adaptor activity / axon terminus / cytoskeleton organization / T-tubule / ERK1 and ERK2 cascade / transcription coregulator binding / positive regulation of epithelial cell proliferation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / MAPK6/MAPK4 signaling / phospholipid binding / positive regulation of miRNA transcription / tau protein binding / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Z disc / G1/S transition of mitotic cell cycle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of granulopoiesis / endocytosis / positive regulation of fibroblast proliferation / actin filament binding / cellular response to UV / MAPK cascade / synaptic vesicle / nuclear envelope / cellular response to xenobiotic stimulus / actin cytoskeleton / Clathrin-mediated endocytosis / protein-folding chaperone binding / regulation of gene expression / GTPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / protease binding / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / cellular response to hypoxia / vesicle / Estrogen-dependent gene expression / response to lipopolysaccharide / intracellular iron ion homeostasis
Similarity search - Function
Amphiphysin 2 / Amphiphysin 2, SH3 domain / Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Amphiphysin / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / BAR domain ...Amphiphysin 2 / Amphiphysin 2, SH3 domain / Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Amphiphysin / 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 / Src homology 3 domains / SH3 type barrels. / 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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