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- PDB-1t0y: Solution Structure of a Ubiquitin-Like Domain from Tubulin-bindin... -

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Basic information

Entry
Database: PDB / ID: 1t0y
TitleSolution Structure of a Ubiquitin-Like Domain from Tubulin-binding Cofactor B
Componentstubulin folding cofactor B
KeywordsCHAPERONE / ubiquitin-like / cytoskeleton / microtubule / tubulin / CESG / Structural genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


post-chaperonin tubulin folding pathway / tubulin complex assembly / alpha-tubulin binding / microtubule / cytoplasm
Similarity search - Function
Tubulin-folding cofactor B, N-terminal ubiquitin-like 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 / Ubiquitin-like (UB roll) ...Tubulin-folding cofactor B, N-terminal ubiquitin-like 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 / Ubiquitin-like (UB roll) / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Tubulin-specific chaperone B
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, CARTESIAN MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
AuthorsLytle, B.L. / Peterson, F.C. / Qui, S.H. / Luo, M. / Volkman, B.F. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Solution Structure of a Ubiquitin-like Domain from Tubulin-binding Cofactor B.
Authors: Lytle, B.L. / Peterson, F.C. / Qiu, S.H. / Luo, M. / Zhao, Q. / Markley, J.L. / Volkman, B.F.
History
DepositionApr 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 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_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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tubulin folding cofactor B


Theoretical massNumber of molelcules
Total (without water)13,7441
Polymers13,7441
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 / 100target function
RepresentativeModel #4closest to the average

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Components

#1: Protein tubulin folding cofactor B / tubulin-specific chaperone B / cytoskeleton-associated protein 1 / CKAP1


Mass: 13744.418 Da / Num. of mol.: 1 / Fragment: N-terminal ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: 5O73 or F53F4.3 / Plasmid: pQE30T / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009[pREP4] / References: UniProt: Q20728

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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
1313D 13C-separated NOESY aromatic
NMR detailsText: CHEMICAL SHIFT ASSIGNMENTS WERE OBTAINED FROM STANDARD 3D TRIPLE-RESONANCE EXPERIMENTS, USING THE AUTOMATED METHOD OF GARANT (C. BARTELS)

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Sample preparation

DetailsContents: 1 mM cofactor B ubiquitin-like domain U-15N, 13C; 20 mM sodium phosphate buffer; 50 mM NaCl
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM NaCl + 20 mM NaPO4 / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1BRUKER BIOSPINcollection
NMRPipe2.1F. DELAGLIOprocessing
XEASY1.4C. BARTELSdata analysis
SPSCAN1.1.0R. GLASERdata analysis
CYANA1.0.6HERRMANN, GUENTERT, WUETHRICHrefinement
XPLOR-NIH2.0.6SCHWIETERS, KUSZEWSKI, TJANDRA, CLORErefinement
RefinementMethod: TORSION ANGLE DYNAMICS, CARTESIAN MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: The C-terminal residues 91-120 were disordered (as evidenced by 15N relaxation data) and were excluded from the model. INITIAL STRUCTURES WERE GENERATED USING THE CANDID MODULE OF CYANA. ...Details: The C-terminal residues 91-120 were disordered (as evidenced by 15N relaxation data) and were excluded from the model. INITIAL STRUCTURES WERE GENERATED USING THE CANDID MODULE OF CYANA. ADDITIONAL NOE ASSIGNMENTS WERE DETERMINED MANUALLY. PHI AND PSI TORSION ANGLE CONSTRAINTS WERE GENERATED FROM CHEMICAL SHIFT DATABASE SEARCHING USING THE PROGRAM TALOS (G. CORNILESCU).
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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