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- PDB-1jas: HsUbc2b -

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Basic information

Entry
Database: PDB / ID: 1jas
TitleHsUbc2b
ComponentsUBIQUITIN-CONJUGATING ENZYME E2-17 KDA
KeywordsLIGASE / ubiquitin conjugation / ubiquitin conjugating enzyme
Function / homology
Function and homology information


synaptonemal complex organization / negative regulation of post-translational protein modification / positive regulation of reciprocal meiotic recombination / chiasma assembly / sperm axoneme assembly / HULC complex / meiotic telomere clustering / protein K11-linked ubiquitination / XY body / negative regulation of cAMP-mediated signaling ...synaptonemal complex organization / negative regulation of post-translational protein modification / positive regulation of reciprocal meiotic recombination / chiasma assembly / sperm axoneme assembly / HULC complex / meiotic telomere clustering / protein K11-linked ubiquitination / XY body / negative regulation of cAMP-mediated signaling / postreplication repair / E2 ubiquitin-conjugating enzyme / negative regulation of reproductive process / negative regulation of developmental process / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / ectopic germ cell programmed cell death / protein autoubiquitination / protein K48-linked ubiquitination / response to UV / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / replication fork / Recognition of DNA damage by PCNA-containing replication complex / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / chromatin organization / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / in utero embryonic development / protein stabilization / protein ubiquitination / response to xenobiotic stimulus / DNA repair / apoptotic process / DNA damage response / ubiquitin protein ligase binding / chromatin / negative regulation of apoptotic process / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiura, T. / Klaus, W. / Ross, A. / Guentert, P. / Senn, H.
CitationJournal: J.Biomol.NMR / Year: 2002
Title: The NMR structure of the class I human ubiquitin-conjugating enzyme 2b
Authors: Miura, T. / Klaus, W. / Ross, A. / Guentert, P. / Senn, H.
History
DepositionMay 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2-17 KDA


Theoretical massNumber of molelcules
Total (without water)17,3281
Polymers17,3281
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 / 100target function
Representative

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Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2-17 KDA


Mass: 17328.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P63146, ubiquitin-protein ligase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
1323D 13C-separated NOESY
1424D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1UL-13C, UL-15N; 75 mM ammonium acetate (deut.), 100 mM ammonium sulphate, pH 6.790% H2O/10% D2O
2UL-13C, 75 mM ammonium acetate (deut.), 100 mM ammonium sulphate, pH 6.7100% D2O
Sample conditionspH: 6.7 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6variouscollection
NMRPipe1.7F. Delaglioprocessing
DYANA1.65P. Guentert et alstructure solution
DYANA1.65P. Guentert et alrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: CANDID: automated NOE cross peak assignment
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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