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- PDB-2kvr: Solution NMR structure of human ubiquitin specific protease Usp7 ... -

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Basic information

Entry
Database: PDB / ID: 2kvr
TitleSolution NMR structure of human ubiquitin specific protease Usp7 UBL domain (residues 537-664). NESG target hr4395c/ SGC-Toronto
ComponentsUbiquitin carboxyl-terminal hydrolase 7
KeywordsPROTEIN BINDING / usp7 / ubiquitin-like domain / UBL / ubiquitin specific protease / Host-virus interaction / Hydrolase / Nucleus / Protease / Thiol protease / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / SGC
Function / homology
Function and homology information


regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity ...regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / negative regulation of TORC1 signaling / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / regulation of protein stability / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / PML body / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Degradation / rhythmic process / p53 binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / protein stabilization / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. ...Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBezsonova, I. / Lemak, A. / Avvakumov, G. / Xue, S. / Dhe-Paganon, S. / Montelione, G.T. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG) / Structural Genomics Consortium (SGC)
Citation
Journal: To be Published
Title: solution structure of the ubiquitin specific protease Usp7 ubiquitin-like domain
Authors: Bezsonova, I. / Lemak, A. / Avvakumov, G. / Xue, S. / Dhe-Paganon, S. / Montelione, G.T. / Arrowsmith, C.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionMar 25, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7


Theoretical massNumber of molelcules
Total (without water)15,1841
Polymers15,1841
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)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 7 / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7 / Deubiquitinating enzyme 7 / ...Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7 / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease


Mass: 15184.020 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain (residues 537-664)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, EC: 3.1.2.15

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HBHA(CO)NH
1613D CBCA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D aromatic 1H-13C NOESY

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Sample preparation

DetailsContents: 0.8-1.2 mM [U-100% 13C; U-100% 15N] protein, 20 mM sodium phosphate, pH 7.0, 250 mM sodium chloride, 2 mM DTT, 0.5 mM PMSF, 1 mM benzamidine, 1 mM TCEP, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMprotein-1[U-100% 13C; U-100% 15N]0.8-1.21
20 mMsodium phosphate, pH 7.0-21
250 mMsodium chloride-31
2 mMDTT-41
0.5 mMPMSF-51
1 mMbenzamidine-61
1 mMTCEP-71
Sample conditionsIonic strength: 250 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Frank Delaglioprocessing
ABACUSA. Lemakchemical shift assignment
CYANA2.1Peter Guntertstructure solution
SparkyT. D. Goddard and D. G. Knellerdata analysis
CYANA2.1Peter Guntertrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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