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- PDB-1tte: The Structure of a Class II ubiquitin-conjugating enzyme, Ubc1. -

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Basic information

Entry
Database: PDB / ID: 1tte
TitleThe Structure of a Class II ubiquitin-conjugating enzyme, Ubc1.
ComponentsUbiquitin-conjugating enzyme E2-24 kDa
KeywordsLIGASE / Ubc1 / E2 / ubiquitin-dependent degradation
Function / homology
Function and homology information


vesicle organization / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity / : / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP binding ...vesicle organization / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity / : / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP binding / nucleus / cytosol
Similarity search - Function
Ubiquitin-conjugating enzyme, C-terminal fungi / Fungal ubiquitin-associated domain / Ubiquitin-associated (UBA) domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / UBA-like superfamily / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 ...Ubiquitin-conjugating enzyme, C-terminal fungi / Fungal ubiquitin-associated domain / Ubiquitin-associated (UBA) domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / UBA-like superfamily / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Helicase, Ruva Protein; domain 3 / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsMerkley, N. / Shaw, G.S.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Solution structure of the flexible class II ubiquitin-conjugating enzyme Ubc1 provides insights for polyubiquitin chain assembly.
Authors: Merkley, N. / Shaw, G.S.
History
DepositionJun 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2-24 kDa


Theoretical massNumber of molelcules
Total (without water)24,1921
Polymers24,1921
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Ubiquitin-conjugating enzyme E2-24 kDa / Ubiquitin-protein ligase / Ubiquitin carrier protein


Mass: 24192.223 Da / Num. of mol.: 1 / Fragment: Ubc1 / Mutation: K93R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBC1, YDR177W, YD9395.10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P21734, ubiquitin-protein ligase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.48mM U-15N,13C Ubc1; 25 mM Tris; 1 mM EDTA, 1mM DITHIOTHREITOL, 150 mM NaCl90 % H2O, 10% H2O
20.48 mM U-15N Ubc1; 25 mM Tris; 1 mM, 1 mM EDTA, 1mM DTT, 150 mM NaCl90% H2O/10% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 7.5 / Pressure: Ambient / Temperature: 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian UNITYVarianUNITY5003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenrefinement
NMRPipe2.1F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
Pipp/Stapp4.3.3Garrett, D.S., Powers, R., Gronenborn, A.M. & Clore, G.Mdata analysis
VNMR6.1CVarian Inccollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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