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- PDB-6xxu: Solution NMR structure of the native form of UbcH7 (UBE2L3) -

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Basic information

Entry
Database: PDB / ID: 6xxu
TitleSolution NMR structure of the native form of UbcH7 (UBE2L3)
ComponentsUbiquitin-conjugating enzyme E2 L3
KeywordsPROTEIN TRANSPORT / UbcH7 / E2 Enzyme / UBC / UBE2L3 / Solution NMR Spectroscopy
Function / homology
Function and homology information


cell cycle phase transition / ubiquitin-protein transferase activator activity / protein K11-linked ubiquitination / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / ubiquitin conjugating enzyme activity / ubiquitin ligase complex ...cell cycle phase transition / ubiquitin-protein transferase activator activity / protein K11-linked ubiquitination / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of protein ubiquitination / Regulation of TNFR1 signaling / protein modification process / Regulation of necroptotic cell death / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process / cell population proliferation / transcription coactivator activity / protein ubiquitination / ubiquitin protein ligase binding / regulation of DNA-templated transcription / enzyme binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / 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 L3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsMarousis, K.D. / Seliami, A. / Birkou, M. / Episkopou, V. / Spyroulias, G.A.
Funding support Greece, 1items
OrganizationGrant numberCountry
General Secretariat for Research and Technology (GSRT)MIS 5005906 Greece
CitationJournal: Biomol.Nmr Assign. / Year: 2020
Title: 1H,13C,15N backbone and side-chain resonance assignment of the native form of UbcH7 (UBE2L3) through solution NMR spectroscopy.
Authors: Marousis, K.D. / Birkou, M. / Asimakopoulou, A. / Spyroulias, G.A.
History
DepositionJan 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 L3


Theoretical massNumber of molelcules
Total (without water)17,8901
Polymers17,8901
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, HPLC/FPLC gel filtrtation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9260 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 21target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 L3 / E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin- ...E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin-conjugating enzyme E2-F1 / Ubiquitin-protein ligase L3


Mass: 17889.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L3, UBCE7, UBCH7 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68036, E2 ubiquitin-conjugating enzyme

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
131isotropic13D HNHA
1102isotropic12D 1H-13C HSQC
142isotropic13D HN(CA)CB
152isotropic13D CBCA(CO)NH
162isotropic13D HNCA
192isotropic13D HN(CO)CA
172isotropic13D 1H-13C NOESY aliphatic
1122isotropic13D 1H-13C NOESY aromatic
1112isotropic13D (H)CCH-TOCSY
182isotropic13D HNCO
1202isotropic13D HN(CA)CO
1192isotropic13D HBHA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.9 mM [U-99% 15N] UbcH7 E2 Enzyme, 50 mM potassium phosphate, 0.25 mM DSS, 90% H2O/10% D2O15N-Sample90% H2O/10% D2O
solution20.9 mM [U-99% 13C; U-99% 15N] UbcH7 E2 Enzyme, 50 mM potassium phosphate, 0.25 mM DSS, 90% H2O/10% D2O13C/15N-Sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMUbcH7 E2 Enzyme[U-99% 15N]1
50 mMpotassium phosphatenatural abundance1
0.25 mMDSSnatural abundance1
0.9 mMUbcH7 E2 Enzyme[U-99% 13C; U-99% 15N]2
50 mMpotassium phosphatenatural abundance2
0.25 mMDSSnatural abundance2
Sample conditionsIonic strength: 50 mM / Label: Conditions-1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz / Details: TCI Probe

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4Keller and Wuthrichchemical shift assignment
DYANAGuntert, Braun and Wuthrichstructure calculation
Amber5Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 21 / Conformers submitted total number: 21

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