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- PDB-2kly: Solution structure of human ubiquitin conjugating enzyme Ube2g2 -

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Basic information

Entry
Database: PDB / ID: 2kly
TitleSolution structure of human ubiquitin conjugating enzyme Ube2g2
ComponentsUbiquitin-conjugating enzyme E2 G2
KeywordsLIGASE / alpha beta fold / ATP-binding / Nucleotide-binding / Ubl conjugation pathway
Function / homology
Function and homology information


negative regulation of retrograde protein transport, ER to cytosol / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / cellular response to interferon-beta / protein K48-linked ubiquitination / ERAD pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / lipid droplet / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation ...negative regulation of retrograde protein transport, ER to cytosol / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / cellular response to interferon-beta / protein K48-linked ubiquitination / ERAD pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / lipid droplet / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / endoplasmic reticulum / ATP binding / identical protein binding / cytosol
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 G2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to mean, model 1
AuthorsJu, T. / Bocik, W. / Majumdar, A. / Tolman, J.R.
CitationJournal: Proteins / Year: 2010
Title: Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2.
Authors: Ju, T. / Bocik, W. / Majumdar, A. / Tolman, J.R.
History
DepositionJul 10, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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 G2


Theoretical massNumber of molelcules
Total (without water)18,7771
Polymers18,7771
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)10 / 10010 structures for lowest energy
RepresentativeModel #1closest to mean

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 G2 / Ubiquitin-protein ligase G2 / Ubiquitin carrier protein G2


Mass: 18777.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2G2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60604, ubiquitin-protein ligase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1312D NOESY
1413D HNHA
152IPAP-HSQC
163IPAP-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-99% 13C; U-99% 15N] Human ubiquitin-conjugating enzyme E2G2 isoform 1, 90% H2O, 10% D2O90% H2O/10% D2O
20.7 mM [U-99% 15N] Human ubiquitin-conjugating enzyme E2G2 isoform 1, 90% H2O, 10% D2O; 8 mg/ml bacteriophage Pf190% H2O, 10% D2O; 8 mg/ml bacteriophage Pf1
31.0 mM [U-99% 13C; U-99% 15N] Human ubiquitin-conjugating enzyme E2G2 isoform 1, 90% H2O, 10% D2O; 4.5% stretched polyacrylamide gel90% H2O, 10% D2O; 4.5% stretched polyacrylamide gel
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMHuman ubiquitin-conjugating enzyme E2G2 isoform 1-1[U-99% 13C; U-99% 15N]1
0.7 mMHuman ubiquitin-conjugating enzyme E2G2 isoform 1-2[U-99% 15N]2
1.0 mMHuman ubiquitin-conjugating enzyme E2G2 isoform 1-3[U-99% 13C; U-99% 15N]3
Sample conditionsIonic strength: 50mM NaCl / pH: 7.0 / Pressure: 1 atm / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA8001
Bruker Avance IIBrukerAVANCE II6002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Refinement by CNS/ARIA
NMR representativeSelection criteria: closest to mean
NMR ensembleConformer selection criteria: 10 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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