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- PDB-2m17: ubiquitin-like domain-containing C-terminal domain phosphatase (U... -

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Basic information

Entry
Database: PDB / ID: 2m17
Titleubiquitin-like domain-containing C-terminal domain phosphatase (UBLCP1)
ComponentsUbiquitin-like domain-containing CTD phosphatase 1
KeywordsHYDROLASE / ubiquitin-like domain-containing C-terminal domain phosphatase (UBLCP1)
Function / homology
Function and homology information


regulation of proteasome assembly / proteasome regulatory particle binding / negative regulation of ATP-dependent activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / protein dephosphorylation / nucleolus / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
HAD-superfamily hydrolase, subfamily IIID / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / HAD superfamily / HAD-like superfamily / Ubiquitin-like (UB roll) / Ubiquitin family ...HAD-superfamily hydrolase, subfamily IIID / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / HAD superfamily / HAD-like superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like domain-containing CTD phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsLee, W. / Yun, J.
CitationJournal: Plos One / Year: 2013
Title: Solution Structure and Rpn1 Interaction of the UBL Domain of Human RNA Polymerase II C-Terminal Domain Phosphatase.
Authors: Yun, J.H. / Ko, S. / Lee, C.K. / Cheong, H.K. / Cheong, C. / Yoon, J.B. / Lee, W.
History
DepositionNov 19, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn / 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_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-like domain-containing CTD phosphatase 1


Theoretical massNumber of molelcules
Total (without water)8,9961
Polymers8,9961
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin-like domain-containing CTD phosphatase 1 / Nuclear proteasome inhibitor UBLCP1


Mass: 8995.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBLCP1 / Plasmid: pGEX 4T-1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WVY7, protein-serine/threonine phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D HNCO
1513D CBCA(CO)NH
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D HBHA(CO)NH

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Sample preparation

DetailsContents: 0.6 mM [U-15N] protein_1, 0.6 mM [U-13C; U-15N] protein_1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMentity_1-1[U-15N]1
0.6 mMentity_1-2[U-13C; U-15N]1
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / 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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