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- PDB-2i50: Solution Structure of Ubp-M Znf-UBP domain -

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Basic information

Entry
Database: PDB / ID: 2i50
TitleSolution Structure of Ubp-M Znf-UBP domain
ComponentsUbiquitin carboxyl-terminal hydrolase 16
KeywordsHYDROLASE / ALPHA/BETA ZINC-FINGER / RING-FINGER / Znf-UBP / metalloprotein / ubiquitin-binding protein / USP / ubiquitin
Function / homology
Function and homology information


histone H2A deubiquitinase activity / mitotic nuclear division / monoubiquitinated protein deubiquitination / positive regulation of translational elongation / ribosomal small subunit binding / protein deubiquitination / positive regulation of ribosome biogenesis / ubiquitin binding / protein homotetramerization / histone binding ...histone H2A deubiquitinase activity / mitotic nuclear division / monoubiquitinated protein deubiquitination / positive regulation of translational elongation / ribosomal small subunit binding / protein deubiquitination / positive regulation of ribosome biogenesis / ubiquitin binding / protein homotetramerization / histone binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / transcription coactivator activity / regulation of cell cycle / Ub-specific processing proteases / cell division / cysteine-type endopeptidase activity / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / proteolysis / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 16 / : / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / 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 16 / : / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / 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. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Papain-like cysteine peptidase superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsPai, M.-T.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Solution structure of the Ubp-M BUZ domain, a highly specific protein module that recognizes the C-terminal tail of free ubiquitin.
Authors: Pai, M.T. / Tzeng, S.R. / Kovacs, J.J. / Keaton, M.A. / Li, S.S. / Yao, T.P. / Zhou, P.
History
DepositionAug 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Determination method: Author defined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6784
Polymers14,4811
Non-polymers1963
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 / 40structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 16 / Ubiquitin thioesterase 16 / Ubiquitin-specific-processing protease 16 / Deubiquitinating enzyme 16 ...Ubiquitin thioesterase 16 / Ubiquitin-specific-processing protease 16 / Deubiquitinating enzyme 16 / Ubiquitin-processing protease UBP-M


Mass: 14481.414 Da / Num. of mol.: 1 / Fragment: Znf-UBP domain, residues 22-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP16 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5T5, EC: 3.1.2.15
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CO)CA
131HN(CA)CB
141HN(COCA)CB
151HNCO
161HN(CA)CO
171HNHA
183(H)CCH-TOCSY
1923D 15N-separated NOESY
11033D 13C-separated NOESY
11142D NOESY
11242D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM U-15N,13C, 25 mM Sodium Phosphate, 100 mM KCl, 95% H2O, 5% D2O95% H2O/5% D2O
21mM U-15N, 25 mM Sodium Phosphate, 100 mM KCl, 95% H2O, 5% D2O95% H2O/5% D2O
31mM U-15N, 13C, 25 mM Sodium Phosphate, 100 mM KCl, 100% D2O100% D2O
4Unlabeled, 25 mM Sodium Phosphate, 100 mM KCl, 100% D2O100% D2O
Sample conditionsIonic strength: 100 mM KCl / pH: 7 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, F.processing
CARA/XEASY1.5.1Keller, R.data analysis
CYANA2.1Guntert, P.structure solution
XPLOR-NIH2.9.7Schwieters, C.D.refinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
Details: Initial structure was calcultated using torsion angle dynamics by CYANA, followed the water refinment with XPLOR-NIH
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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