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- PDB-2l80: Solution Structure of the Zinc Finger Domain of USP13 -

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Basic information

Entry
Database: PDB / ID: 2l80
TitleSolution Structure of the Zinc Finger Domain of USP13
ComponentsUbiquitin carboxyl-terminal hydrolase 13
KeywordsPROTEIN BINDING / Zinc finger / USP13 / Ubiquitin binding
Function / homology
Function and homology information


protein K29-linked deubiquitination / protein K6-linked deubiquitination / maintenance of unfolded protein / positive regulation of ERAD pathway / melanocyte differentiation / BAT3 complex binding / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / proteasome binding / ubiquitin-like protein ligase binding ...protein K29-linked deubiquitination / protein K6-linked deubiquitination / maintenance of unfolded protein / positive regulation of ERAD pathway / melanocyte differentiation / BAT3 complex binding / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / proteasome binding / ubiquitin-like protein ligase binding / protein deubiquitination / ubiquitin binding / regulation of protein stability / autophagy / Regulation of PTEN stability and activity / protein-folding chaperone binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cell population proliferation / regulation of autophagy / protein stabilization / Ub-specific processing proteases / cysteine-type endopeptidase activity / ubiquitin protein ligase binding / regulation of DNA-templated transcription / proteolysis / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / UBA-like domain / : / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / UBA/TS-N domain ...Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / UBA-like domain / : / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / UBA/TS-N domain / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Ubiquitin associated domain / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / 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 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsZhang, Y. / Zhou, C. / Zhou, Z. / Song, A. / Hu, H.
CitationJournal: To be Published
Title: Biochemical Characterization of the Ubiquitin Receptors in USP13 Reveals Different Catalytic Activation of Deubiquitination from Its Analogue USP5
Authors: Zhang, Y. / Song, A. / Zhou, C. / Zhou, Z. / Hu, H.
History
DepositionDec 28, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: 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_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9062
Polymers12,8401
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 13 / USP13 / Deubiquitinating enzyme 13 / Isopeptidase T-3 / ISOT-3 / Ubiquitin thiolesterase 13 / ...USP13 / Deubiquitinating enzyme 13 / Isopeptidase T-3 / ISOT-3 / Ubiquitin thiolesterase 13 / Ubiquitin-specific-processing protease 13


Mass: 12840.424 Da / Num. of mol.: 1
Fragment: Zinc finger Domain, UBP-type, UNP residues 188-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92995
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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
1112D 1H-15N HSQC
1223D HN(CA)CB
1323D CBCA(CO)NH
1413D HNHA
1523D HNCO
1623D C(CO)NH
1723D (H)CCH-TOCSY
1813D 1H-15N NOESY
1923D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-15N] entity; 20mM sodium phosphate; 50mM sodium chloride; 90% H2O/10% D2O90% H2O/10% D2O
21mM [U-100% 13C; U-100% 15N] entity; 20mM sodium phosphate; 50mM sodium chloride; 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
1 mMentity-4[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate-52
50 mMsodium chloride-62
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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