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- PDB-2lva: NMR solution structure of the N-terminal domain of human USP28, N... -

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Basic information

Entry
Database: PDB / ID: 2lva
TitleNMR solution structure of the N-terminal domain of human USP28, Northeast structural genomics consortium target HT8470A
ComponentsUbiquitin carboxyl-terminal hydrolase 28
KeywordsHYDROLASE / UIM / ubiquitin interacting motif / UBA domain / NESG / Northeast structural genomics consortium / SGC / Structural Genomics Consortium / PSI-Biology
Function / homology
Function and homology information


protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / response to ionizing radiation / protein deubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cell population proliferation ...protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / response to ionizing radiation / protein deubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cell population proliferation / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / DNA repair / DNA damage response / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1720 / Ubiquitin-associated (UBA) domain / 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. / UBA-like superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1720 / Ubiquitin-associated (UBA) domain / 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. / UBA-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helicase, Ruva Protein; domain 3 / Helix non-globular / Papain-like cysteine peptidase superfamily / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / restrained molecular dynamics
Model detailslowest energy, model 1
AuthorsLemak, A. / Yee, A. / Houliston, S. / Garcia, M. / Dhe-Paganon, S. / Montelione, G.T. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG) / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: NMR solution structure of the N-terminal domain of human USP28
Authors: Lemak, A. / Yee, A. / Houliston, S. / Garcia, M. / Dhe-Paganon, S. / Montelione, G.T. / Arrowsmith, C.
History
DepositionJun 29, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.2May 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 28


Theoretical massNumber of molelcules
Total (without water)14,2461
Polymers14,2461
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 28 / Deubiquitinating enzyme 28 / Ubiquitin thioesterase 28 / Ubiquitin-specific-processing protease 28


Mass: 14245.727 Da / Num. of mol.: 1 / Fragment: UIM domain residues 22-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D (H)CCH-TOCSY
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] protein, 10 mM mops, 450 mM sodium chloride, 10 uM ZnSO4, 1 mM DTT, 0.01 % NaN3, 1 mM benzamidine, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-13C; U-15N]1
10 mMmops-21
450 mMsodium chloride-31
10 uMZnSO4-41
1 mMDTT-51
0.01 %NaN3-61
1 mMbenzamidine-71
Sample conditionsIonic strength: 450 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FMCLemak,Steren,Llinas, Arrowsmithchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
PSVSBhattacharya and Montelionevalidation
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
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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