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- PDB-2hlw: Solution Structure of the Human Ubiquitin-conjugating Enzyme Vari... -

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Basic information

Entry
Database: PDB / ID: 2hlw
TitleSolution Structure of the Human Ubiquitin-conjugating Enzyme Variant Uev1a
ComponentsUbiquitin-conjugating enzyme E2 variant 1
KeywordsLigase / Signaling Protein / ubiquitin-conjugating enzyme variant / ubiquitin / ubc13 / hubc13 / E2 / polyubiquitination
Function / homology
Function and homology information


: / ubiquitin conjugating enzyme complex / positive regulation of protein K63-linked ubiquitination / postreplication repair / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / regulation of DNA repair / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation ...: / ubiquitin conjugating enzyme complex / positive regulation of protein K63-linked ubiquitination / postreplication repair / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / regulation of DNA repair / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / activated TAK1 mediates p38 MAPK activation / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Aggrephagy / Interleukin-1 signaling / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / cell differentiation / regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 variant 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
Model type detailsminimized average
AuthorsHau, D.D. / Lewis, M.J. / Saltibus, L.F. / Pastushok, L. / Xiao, W. / Spyracopoulos, L.
CitationJournal: Biochemistry / Year: 2006
Title: Structure and interactions of the ubiquitin-conjugating enzyme variant human uev1a: implications for enzymatic synthesis of polyubiquitin chains(,).
Authors: Hau, D.D. / Lewis, M.J. / Saltibus, L.F. / Pastushok, L. / Xiao, W. / Spyracopoulos, L.
History
DepositionJul 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Ubiquitin-conjugating enzyme E2 variant 1


Theoretical massNumber of molelcules
Total (without water)19,3321
Polymers19,3321
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 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 variant 1 / UEV-1 / CROC-1 / Ubiquitin-conjugating enzyme variant Kua / TRAF6-regulated IKK activator 1 beta Uev1A


Mass: 19332.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UEV1 / Plasmid: pGEX-6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13404

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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
131HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM hUev1a U-15N,13C; 50 mM NaH2PO4, 250 mM NaCl, 0.9 mM DTT, 1.7 mM DSS; 90% H2O, 10% D2O90% H2O/10% D2O
20.75mM hUev1a U-15N,U-10% 13C; 50 mM NaH2PO4, 250 mM NaCl, 0.9 mM DTT, 1.7 mM DSS; 90% H2O, 10% D2O90% H2O/10% D2O
30.5mM hUev1a U-15N; 50 mM NaH2PO4, 250 mM NaCl, 0.9 mM DTT, 1.7 mM DSS; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM NaH2PO4, 250 mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 303 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 UNITYVarianUNITY6001
Varian UNITYVarianUNITY8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
NMRPipeunknownDelaglioprocessing
NMRView5.2.2Johnsondata analysis
VNMR6.1Variancollection
Sparky3.11Goddarddata analysis
Procheck3.5.4Laskowskirefinement
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
Details: 2080 NOE-derived distance restraints, 56 JHNHA-derived phi restraints, 69 TALOS-derived phi restraints, 68 TALOS-derived psi restraints, 4 dNa/daN-derived psi restraints, 36 hydrogen bond restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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