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- PDB-2rnd: Structure of the N-terminal BARpeptide in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 2rnd
TitleStructure of the N-terminal BARpeptide in DPC micelles
ComponentsMyc box-dependent-interacting protein 1
KeywordsENDOCYTOSIS / BARpeptide / micelle / NMR-structure / Alternative splicing / Anti-oncogene / Cell cycle / Coiled coil / Cytoplasm / Developmental protein / Differentiation / Disease mutation / Host-virus interaction / Nucleus / Phosphoprotein / SH3 domain
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 / Src homology 3 domains ...Amphiphysin 2 / Amphiphysin 2, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Myc box-dependent-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsLoew, C. / Weininger, U. / Balbach, J.
CitationJournal: Biophys.J. / Year: 2008
Title: Structure and dynamics of helix-0 of the N-BAR domain in lipid micelles and bilayers
Authors: Low, C. / Weininger, U. / Lee, H. / Schweimer, K. / Neundorf, I. / Beck-Sickinger, A.G. / Pastor, R.W. / Balbach, J.
History
DepositionDec 16, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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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)3,7141
Polymers3,7141
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)10 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 3714.424 Da / Num. of mol.: 1 / Fragment: BARpeptide, UNP residues 1-33
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): BL21 / References: UniProt: O00499
Sequence detailsC-TERMINAL TYROSIN 34 FOR CONCENTRATION DETERMINATION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-15N TOCSY
1412D 1H-1H NOESY

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Sample preparation

DetailsContents: 1mM [U-100% 15N] protein, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: entity / Isotopic labeling: [U-100% 15N]
Sample conditionsIonic strength: 0 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.1Linge, O'Donoghue, Nilgesstructure solution
ARIA2.1Linge, O'Donoghue, Nilgesrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 550
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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