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- PDB-2al3: Solution structure and backbone dynamics of an N-terminal ubiquit... -

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Basic information

Entry
Database: PDB / ID: 2al3
TitleSolution structure and backbone dynamics of an N-terminal ubiquitin-like domain in the GLUT4-tethering protein, TUG
ComponentsTUG long isoform
KeywordsENDOCYTOSIS/EXOCYTOSIS / TUG UBL1 Insulin / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


positive regulation of protein modification process / regulation of glucose import / vesicle membrane / extrinsic component of membrane / endomembrane system / endoplasmic reticulum-Golgi intermediate compartment membrane / intracellular protein transport / cytoplasmic vesicle membrane / cytoplasmic side of plasma membrane / glucose homeostasis ...positive regulation of protein modification process / regulation of glucose import / vesicle membrane / extrinsic component of membrane / endomembrane system / endoplasmic reticulum-Golgi intermediate compartment membrane / intracellular protein transport / cytoplasmic vesicle membrane / cytoplasmic side of plasma membrane / glucose homeostasis / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
TUG ubiquitin-like domain / TUG ubiquitin-like domain / UBX domain / UBX domain / UBX domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / Tether containing UBX domain for GLUT4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTettamanzi, M.C. / Yu, C. / Bogan, J.S. / Hodsdon, M.E.
CitationJournal: Protein Sci. / Year: 2006
Title: Solution structure and backbone dynamics of an N-terminal ubiquitin-like domain in the GLUT4-regulating protein, TUG.
Authors: Tettamanzi, M.C. / Yu, C. / Bogan, J.S. / Hodsdon, M.E.
History
DepositionAug 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The missing residues are the results of structural disorder and degradation during the experiments.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUG long isoform


Theoretical massNumber of molelcules
Total (without water)9,9191
Polymers9,9191
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 / 20structures with the least restraint violations
RepresentativeModel #1

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Components

#1: Protein TUG long isoform


Mass: 9919.222 Da / Num. of mol.: 1 / Fragment: N-Terminal Ubiquitin-Like Domain (residues 1-90)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: tug / Plasmid: pGEX-2K / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: GenBank: 37704773, UniProt: Q8VBT9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C/15N-separated NOESY
1213D 13C-separated NOESY
1313D 15N -SEPARATED NOESY

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Sample preparation

DetailsContents: 0.75 mM TUG-UBL1, 20 MM POTASSIUM PHOSPHATE, 20 MM NACL, 0.05% NAN3, 1 UM LUPEPTIN, 1 UM PEPSTATIN, 1 UM PMSF, 1.5 MM PROTEIN, UNIFORM (RANDOM) LABELING WITH 13C, 15N AT KNOWN LABELING
Solvent system: 20 MM POTASSIUM PHOSPHATE, 20 MM NACL, 0.05% NAN3, 1 UM LUPEPTIN, 1 UM PEPSTATIN, 1 UM PMSF, 1.5 MM PROTEIN, UNIFORM (RANDOM) LABELING WITH 13C, 15N AT KNOWN LABELING
Sample conditionsIonic strength: 20 mM NaCl / pH: 7.4 / 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.5P.GUNTERT ET AL.refinement
VNMR6.1Variancollection
NMRDraw2.1F. Delaglio et Aldata analysis
NMRPipeF. Delaglio et Alprocessing
Sparky3.98T. D. Goddard et Aldata analysis
NMRView5.0.4One Moon Scientific, Inc.data analysis
CYANA1.0.5P.GUNTERT ET AL.structure solution
TALOSA. Bax et Alstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 20

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