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- PDB-5vkg: Solution-state NMR structural ensemble of human Tsg101 UEV in com... -

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Basic information

Entry
Database: PDB / ID: 5vkg
TitleSolution-state NMR structural ensemble of human Tsg101 UEV in complex with tenatoprazole
ComponentsTumor susceptibility gene 101 proteinTSG101
Keywordscell cycle/inhibitor / ESCRT-I / inhibitor / cell cycle / cell cycle-inhibitor complex
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
Chem-4N1 / Tumor susceptibility gene 101 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsStrickland, M. / Ehrlich, L.S. / Watanabe, S. / Khan, M. / Strub, M.-P. / Luan, C.H. / Powell, M.D. / Leis, J. / Tjandra, N. / Carter, C.
CitationJournal: Nat Commun / Year: 2017
Title: Tsg101 chaperone function revealed by HIV-1 assembly inhibitors.
Authors: Strickland, M. / Ehrlich, L.S. / Watanabe, S. / Khan, M. / Strub, M.P. / Luan, C.H. / Powell, M.D. / Leis, J. / Tjandra, N. / Carter, C.A.
History
DepositionApr 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor susceptibility gene 101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8912
Polymers16,5591
Non-polymers3311
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, Liquid-chromatography mass spectrometry was used to confirm that 4N1 is attached to Tsg101 via a disulfide bond. NMR spectroscopy also confirmed this.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Tumor susceptibility gene 101 protein / TSG101 / ESCRT-I complex subunit TSG101


Mass: 16559.207 Da / Num. of mol.: 1 / Mutation: M1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Plasmid: pET-28B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q99816
#2: Chemical ChemComp-4N1 / 4-methoxy-1-(5-methoxy-3H-imidazo[4,5-b]pyridin-2-yl)-3,5-dimethyl-2-(sulfanylmethyl)pyridin-1-ium


Mass: 331.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N4O2S

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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
222isotropic22D 1H-13C HSQC aliphatic
131isotropic13D HN(CA)CB
141isotropic13D H(CCO)NH
151isotropic23D 1H-15N NOESY
262isotropic33D 1H-13C NOESY aliphatic
272isotropic23D 1H-13C NOESY aromatic
281isotropic23D 1H-13C-12C filtered NOESY aliphatic
191isotropic13D CBCA(CO)NH
1101isotropic13D C(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.6 mM [U-98% 13C; U-98% 15N] Tsg101, 0.6 mM Tenatoprazole, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2OTenatoprazole (dissolved in DMSO) was allowed to react covalently with Tsg101, which was followed by buffer exchange to remove excess DMSO and tenatoprazole.15N13C_H2O93% H2O/7% D2O
solution20.6 mM [U-13C; U-15N] Tsg101, 0.6 mM Tenatoprazole, 20 mM potassium phosphate, 50 mM sodium chloride, 100% D2O13C-NOESY experiments were carried out using this sample.15N13C_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMTsg101[U-98% 13C; U-98% 15N]1
0.6 mMTenatoprazolenatural abundance1
20 mMpotassium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.6 mMTsg101[U-13C; U-15N]2
0.6 mMTenatoprazolenatural abundance2
20 mMpotassium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10.1 M15N13C_H2O_cond5.8 1 atm300 K
20.1 mM15N13C_D2O_cond5.8 pH*1 atm300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Cryoprobe
Bruker AVANCEBrukerAVANCE8002Cryoprobe
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
NMRPipe8.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDraw8.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Analysis2.4.2CCPNpeak picking
Analysis2.4.2CCPNchemical shift assignment
Analysis2.4.2CCPNdata analysis
X-PLOR NIH2.37.7Schwieters, Kuszewski, Tjandra and Clorerefinement
PSVS1.5Bhattacharya and Montelionedata analysis
Gaussian9Gaussian, Inc.geometry optimization
TALOS-N4.12Yang Shen and Ad Baxdata analysis
X-PLOR NIH2.37.7Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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