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- PDB-1ttn: Solution structure of the ubiquitin-like domain of human DC-UBP f... -

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Basic information

Entry
Database: PDB / ID: 1ttn
TitleSolution structure of the ubiquitin-like domain of human DC-UBP from dendritic cells
Componentsdendritic cell-derived ubiquitin-like protein
KeywordsSIGNALING PROTEIN / Ubiquitin-like Domain / DC-UBP / Solution Structure
Function / homology
Function and homology information


DC-UbP/UBTD2, N-terminal domain / DC-UbP/UBTD2, N-terminal domain superfamily / Ubiquitin domain-containing protein 1/2 / Ubiquitin-binding domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily ...DC-UbP/UBTD2, N-terminal domain / DC-UbP/UBTD2, N-terminal domain superfamily / Ubiquitin domain-containing protein 1/2 / Ubiquitin-binding domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsHu, H.Y.
CitationJournal: Protein Sci. / Year: 2005
Title: Solution structure of the ubiquitin-like domain of human DC-UbP from dendritic cells
Authors: Gao, Y.G. / Song, A.X. / Shi, Y.H. / Chang, Y.G. / Liu, S.X. / Yu, Y.Z. / Cao, X.T. / Lin, D.H. / Hu, H.Y.
History
DepositionJun 23, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: dendritic cell-derived ubiquitin-like protein


Theoretical massNumber of molelcules
Total (without water)12,1811
Polymers12,1811
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)15 / 150structures with the lowest energy
RepresentativeModel #15minimized average structure

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Components

#1: Protein dendritic cell-derived ubiquitin-like protein / DC-UBP


Mass: 12180.951 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8WUN7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
131HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM ubiquitin-like domain of DC-UBP ,10mM NaAc, 100mM NaCl, 5mM DTT, 0.02% sodium azide92% H2O, 8% D2O
21.2mM ubiquitin-like domain of DC-UBP ,10mM NaAc, 100mM NaCl, 5mM DTT, 0.02% sodium azideD2O
Sample conditionspH: 5.6 / 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
XwinNMRVariancollection
NMRPipeFrank Delaglioprocessing
NMRView5Bruce Johnsondata analysis
CNS1.1A.T.Brunger et al.refinement
ARIA1.2Jens Linge et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on 901 NOE-derived distance constraints,83 dihedral angle restraints,60 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 15

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