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- PDB-2lug: Solution NMR structure of a S72-S107 peptide of 18.5kDa murine my... -

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Basic information

Entry
Database: PDB / ID: 2lug
TitleSolution NMR structure of a S72-S107 peptide of 18.5kDa murine myelin basic protein (MBP) in association with dodecylphosphocholine micelles
ComponentsMyelin basic protein
KeywordsLIPID BINDING PROTEIN / intrinsically disordered proteins / dodecylphosphocholine micelles / myelin membrane
Function / homology
Function and homology information


compact myelin / structural constituent of myelin sheath / internode region of axon / negative regulation of heterotypic cell-cell adhesion / negative regulation of axonogenesis / membrane organization / positive regulation of chemokine (C-X-C motif) ligand 2 production / maintenance of blood-brain barrier / myelination / cell periphery ...compact myelin / structural constituent of myelin sheath / internode region of axon / negative regulation of heterotypic cell-cell adhesion / negative regulation of axonogenesis / membrane organization / positive regulation of chemokine (C-X-C motif) ligand 2 production / maintenance of blood-brain barrier / myelination / cell periphery / cell projection / response to progesterone / sensory perception of sound / response to toxic substance / positive regulation of interleukin-6 production / MAPK cascade / myelin sheath / protease binding / calmodulin binding / neuronal cell body / cell surface / protein-containing complex / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Myelin basic protein / Myelin basic protein / Myelin basic protein signature.
Similarity search - Domain/homology
: / Myelin basic protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAhmed, M.A.M. / De Avila, M. / Polverini, E. / Bessonov, K. / Bamm, V.V. / Harauz, G.
CitationJournal: Biochemistry / Year: 2012
Title: Solution Nuclear Magnetic Resonance Structure and Molecular Dynamics Simulations of a Murine 18.5 kDa Myelin Basic Protein Segment (S72-S107) in Association with Dodecylphosphocholine Micelles.
Authors: Ahmed, M.A. / De Avila, M. / Polverini, E. / Bessonov, K. / Bamm, V.V. / Harauz, G.
History
DepositionJun 13, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myelin basic protein


Theoretical massNumber of molelcules
Total (without water)3,9771
Polymers3,9771
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)10 / 10500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Myelin basic protein


Mass: 3977.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mbp / Plasmid: pET-SUMO vector / Production host: Escherichia coli (E. coli) / References: UniProt: F6VME3, UniProt: P04370*PLUS

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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 HNCO
1313D HN(CA)CO
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HACAN
1713D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1.47 mM [U-100% 13C; U-100% 15N] S72-S107 MBP peptide, 50 mM potassium phosphate, 100 mM Deuterated Dodecylphosphocholine, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.47 mMS72-S107 MBP peptide-1[U-100% 13C; U-100% 15N]1
50 mMpotassium phosphate-21
100 mMDodecylphosphocholine-3Deuterated1
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 285 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichchemical shift assignment
TALOSCornilescu, Delaglio and Baxbackbone phi/psi torsion angle prediction
TALOSCornilescu, Delaglio and Baxstructure solution
CS-ROSETTAShen, Lange, Delaglio, Rossi, Aramini, Liu, Eletsky, Wu, Singarapu, Lemak, ... and Baxstructure solution
CS-ROSETTAShen, Lange, Delaglio, Rossi, Aramini, Liu, Eletsky, Wu, Singarapu, Lemak, ... and Baxrefinement
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: 10500 / Conformers submitted total number: 10

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