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- PDB-2uzg: Zf-UBP domain of VDU1 -

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Basic information

Entry
Database: PDB / ID: 2uzg
TitleZf-UBP domain of VDU1
ComponentsUBIQUITIN CARBOXYL-TERMINAL HYDROLASE 33
KeywordsHYDROLASE / UBL CONJUGATION PATHWAY / DE-UBIQUITINATION / ALTERNATIVE SPLICING / METAL-BINDING / THIOL PROTEASE / UBL CONJUGATION / ZINC / VDU1 / ZF-UBP / PROTEASE / ZINC-FINGER
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / cysteine-type deubiquitinase activity => GO:0004843 / protein K48-linked deubiquitination / regulation of G protein-coupled receptor signaling pathway / VCB complex / protein K63-linked deubiquitination / protein deubiquitination / centrosome duplication / cellular response to starvation / negative regulation of protein binding ...small GTPase binding => GO:0031267 / cysteine-type deubiquitinase activity => GO:0004843 / protein K48-linked deubiquitination / regulation of G protein-coupled receptor signaling pathway / VCB complex / protein K63-linked deubiquitination / protein deubiquitination / centrosome duplication / cellular response to starvation / negative regulation of protein binding / regulation of autophagy / G protein-coupled receptor binding / axon guidance / Regulation of expression of SLITs and ROBOs / endocytosis / cell migration / positive regulation of protein binding / cell body / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / Ub-specific processing proteases / cysteine-type endopeptidase activity / focal adhesion / centrosome / perinuclear region of cytoplasm / Golgi apparatus / zinc ion binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / 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. ...Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / 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 33
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CNS
AuthorsAllen, M.D. / Bycroft, M.
CitationJournal: Protein Sci. / Year: 2007
Title: The Solution Structure of the Znf Ubp Domain of Usp33/Vdu1.
Authors: Allen, M.D. / Bycroft, M.
History
DepositionApr 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1254
Polymers10,9281
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 / 20NO VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 33 / UBIQUITIN THIOESTERASE 33 / UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 33 / DEUBIQUITINATING ENZYME 33 ...UBIQUITIN THIOESTERASE 33 / UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 33 / DEUBIQUITINATING ENZYME 33 / VHL-INTERACTING DEUBIQUITINATING ENZYME 1


Mass: 10928.337 Da / Num. of mol.: 1 / Fragment: RESIDUES 36-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q8TEY7
#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 detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED AND UNLABELLED PROTEIN

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 60 mM / pH: 6.5 / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
ANSIG3.3structure solution
RefinementMethod: CNS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: NO VIOLATIONS / Conformers calculated total number: 20 / Conformers submitted total number: 20

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