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- PDB-1kpq: Structure of the Tsg101 UEV domain -

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Basic information

Entry
Database: PDB / ID: 1kpq
TitleStructure of the Tsg101 UEV domain
ComponentsTumor susceptibility gene 101 proteinTSG101
KeywordsCELL CYCLE / E2 FOLD
Function / homology
Function and homology information


positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / Flemming body / virion binding / endosome to lysosome transport / negative regulation of epidermal growth factor receptor signaling pathway / viral budding via host ESCRT complex / autophagosome maturation / viral release from host cell / keratinocyte differentiation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / HCMV Late Events / ubiquitin binding / regulation of cell growth / macroautophagy / Late endosomal microautophagy / protein modification process / Budding and maturation of HIV virion / transcription corepressor activity / calcium-dependent protein binding / late endosome / late endosome membrane / early endosome membrane / early endosome / endosome membrane / regulation of cell cycle / endosome / cell cycle / cell division / negative regulation of cell population proliferation / centrosome / ubiquitin protein ligase binding / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / UEV domain / UEV domain profile. / ESCRT assembly domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme E2, catalytic domain homologues ...Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / UEV domain / UEV domain profile. / ESCRT assembly domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Tumor susceptibility gene 101 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DYANA
AuthorsPornillos, O. / Alam, S.L. / Rich, R.L. / Myszka, D.G. / Davis, D.R. / Sundquist, W.I.
CitationJournal: EMBO J. / Year: 2002
Title: Structure and functional interactions of the Tsg101 UEV domain.
Authors: Pornillos, O. / Alam, S.L. / Rich, R.L. / Myszka, D.G. / Davis, D.R. / Sundquist, W.I.
History
DepositionJan 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2002Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor susceptibility gene 101 protein


Theoretical massNumber of molelcules
Total (without water)16,6331
Polymers16,6331
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)15 / 20Structures with the lowest DYANA target function
RepresentativeModel #1lowest dyana target function

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Components

#1: Protein Tumor susceptibility gene 101 protein / TSG101 / Tsg101


Mass: 16633.352 Da / Num. of mol.: 1 / Fragment: UEV domain, residues 1-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: tsg101 / Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99816

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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

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Sample preparation

DetailsContents: ~1.5 mM Tsg101 UEV; 20 mM sodium phosphate pH 5.5; 50 mM NaCl
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 5.5 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameClassification
Felixprocessing
DYANAstructure solution
DYANArefinement
Sparkydata analysis
RefinementMethod: DYANA / Software ordinal: 1
NMR representativeSelection criteria: lowest dyana target function
NMR ensembleConformer selection criteria: Structures with the lowest DYANA target function
Conformers calculated total number: 20 / Conformers submitted total number: 15

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