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- PDB-1wjn: Solution structure of the C-terminal ubiquitin-like domain of mou... -

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Basic information

Entry
Database: PDB / ID: 1wjn
TitleSolution structure of the C-terminal ubiquitin-like domain of mouse tubulin-specific chaperone e
ComponentsTubulin-folding protein TBCE
KeywordsCHAPERONE / ubiquitin-like domain / progressive motor neuropathy / tubulin-folding protein TBCE / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


peripheral nervous system neuron axonogenesis / post-chaperonin tubulin folding pathway / muscle atrophy / tubulin complex assembly / alpha-tubulin binding / developmental growth / axonogenesis / adult locomotory behavior / mitotic spindle organization / post-embryonic development ...peripheral nervous system neuron axonogenesis / post-chaperonin tubulin folding pathway / muscle atrophy / tubulin complex assembly / alpha-tubulin binding / developmental growth / axonogenesis / adult locomotory behavior / mitotic spindle organization / post-embryonic development / microtubule cytoskeleton organization / unfolded protein binding / protein folding / cytoskeleton / cytoplasm
Similarity search - Function
TBCE, ubiquitin-like (Ubl) domain / Ubiquitin-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Leucine-rich repeat domain superfamily ...TBCE, ubiquitin-like (Ubl) domain / Ubiquitin-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Leucine-rich repeat domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Tubulin-specific chaperone E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSato, M. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the C-terminal ubiquitin-like domain of mouse tubulin-specific chaperone e
Authors: Sato, M. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tubulin-folding protein TBCE


Theoretical massNumber of molelcules
Total (without water)10,7021
Polymers10,7021
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 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Tubulin-folding protein TBCE / tubulin-specific chaperone e


Mass: 10702.256 Da / Num. of mol.: 1 / Fragment: ubiquitin like-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 2610206D02 / Plasmid: P040301-91 / References: UniProt: Q8CIV8

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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

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Sample preparation

DetailsContents: 1.1mM ubiquitin-like domain U-15N,13C; 20mM d-Tris-HCl; 200mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 220mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.8994Kobayashi, N.data analysis
CYANA2.0.17Guentert, P.structure solution
CYANA2.0.17Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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