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- PDB-2mt6: Solution structure of the human ubiquitin conjugating enzyme Ube2w -

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Basic information

Entry
Database: PDB / ID: 2mt6
TitleSolution structure of the human ubiquitin conjugating enzyme Ube2w
ComponentsUbiquitin-conjugating enzyme E2 W
KeywordsLIGASE / ubiquitin / ube2w / E2 / ubiquitin conjugating enzyme
Function / homology
Function and homology information


N-terminal E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / cellular response to misfolded protein / E2 ubiquitin-conjugating enzyme / protein quality control for misfolded or incompletely synthesized proteins / protein monoubiquitination / ubiquitin conjugating enzyme activity / antiviral innate immune response / negative regulation of TORC1 signaling / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...N-terminal E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / cellular response to misfolded protein / E2 ubiquitin-conjugating enzyme / protein quality control for misfolded or incompletely synthesized proteins / protein monoubiquitination / ubiquitin conjugating enzyme activity / antiviral innate immune response / negative regulation of TORC1 signaling / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA repair / ubiquitin protein ligase binding / nucleoplasm / ATP binding / nucleus / cytoplasm
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 W
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsVittal, V. / Shi, L. / Wenzel, D.M. / Brzovic, P.S. / Klevit, R.E.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Intrinsic disorder drives N-terminal ubiquitination by Ube2w.
Authors: Vittal, V. / Shi, L. / Wenzel, D.M. / Scaglione, K.M. / Duncan, E.D. / Basrur, V. / Elenitoba-Johnson, K.S. / Baker, D. / Paulson, H.L. / Brzovic, P.S. / Klevit, R.E.
History
DepositionAug 14, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 W


Theoretical massNumber of molelcules
Total (without water)17,3511
Polymers17,3511
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)20 / 16000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 W / N-terminus-conjugating E2 / Ubiquitin carrier protein W / Ubiquitin-conjugating enzyme 16 / UBC-16 ...N-terminus-conjugating E2 / Ubiquitin carrier protein W / Ubiquitin-conjugating enzyme 16 / UBC-16 / Ubiquitin-protein ligase W


Mass: 17350.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2W, UBC16 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96B02, ubiquitin-protein ligase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1612D 1H-15N HSQC

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Sample preparation

DetailsContents: 200-400 uM [U-100% 13C; U-100% 15N] Ube2w, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: uM / Component: Ube2w-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] / Conc. range: 200-400
Sample conditionsIonic strength: 150 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker INOVABrukerINOVA6002

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Processing

NMR software
NameDeveloperClassification
CS-ROSETTAShen, Vernon, Baker and Baxstructure solution
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 16000 / Conformers submitted total number: 20

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