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- PDB-6ir0: Zinc finger domain of the human DTX protein -

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Open data


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Basic information

Entry
Database: PDB / ID: 6ir0
TitleZinc finger domain of the human DTX protein
ComponentsProbable E3 ubiquitin-protein ligase DTX2
KeywordsLIGASE / RING finger / DTX / zinc finger
Function / homology
Function and homology information


Notch signaling pathway / Activated NOTCH1 Transmits Signal to the Nucleus / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / nuclear membrane / protein ubiquitination / zinc ion binding / nucleoplasm / cytoplasm
Similarity search - Function
Deltex, C-terminal / Deltex family / Deltex, C-terminal domain superfamily / Deltex C-terminal domain / WWE domain, subgroup / Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis. / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. ...Deltex, C-terminal / Deltex family / Deltex, C-terminal domain superfamily / Deltex C-terminal domain / WWE domain, subgroup / Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis. / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable E3 ubiquitin-protein ligase DTX2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiyamoto, K.
CitationJournal: Protein Sci. / Year: 2019
Title: Zinc finger domain of the human DTX protein adopts a unique RING fold.
Authors: Miyamoto, K. / Fujiwara, Y. / Saito, K.
History
DepositionNov 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
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 / _struct_conn.pdbx_dist_value
Revision 1.3May 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: Probable E3 ubiquitin-protein ligase DTX2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3113
Polymers8,1801
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Cysteine modification
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4800 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Probable E3 ubiquitin-protein ligase DTX2 / Protein deltex-2 / hDTX2 / RING finger protein 58 / RING-type E3 ubiquitin transferase DTX2


Mass: 8180.370 Da / Num. of mol.: 1 / Fragment: Zinc finger domain / Mutation: I36L / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q86UW9, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM U-13C, 15N Zinc finger domain of the human DTX protein, 90% H2O/10% D2O
Label: zinc finger / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Zinc finger domain of the human DTX protein / Isotopic labeling: U-13C, 15N
Sample conditionsIonic strength: 70 mM / Label: conditions_1 / pH: 6.9 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 4 / Details: ver. 2.1
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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