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- PDB-5xek: C-terminal zinc finger of RING finger protein 141 -

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Basic information

Entry
Database: PDB / ID: 5xek
TitleC-terminal zinc finger of RING finger protein 141
ComponentsRING finger protein 141
KeywordsMETAL BINDING PROTEIN / RING finger protein 141 / Zinc Finger
Function / homology
Function and homology information


protein autoubiquitination / ubiquitin-protein transferase activity / regulation of DNA-templated transcription / membrane / metal ion binding
Similarity search - Function
RNF141, RING finger, HC subclass / : / Ring finger domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type ...RNF141, RING finger, HC subclass / : / Ring finger domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / 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
RING finger protein 141
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiyamoto, K.
CitationJournal: To Be Published
Title: C-terminal zinc finger of RING finger protein 141
Authors: Miyamoto, K.
History
DepositionApr 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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
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: RING finger protein 141
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0523
Polymers4,9211
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3790 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/peptide RING finger protein 141 / / Zinc finger protein 230


Mass: 4920.788 Da / Num. of mol.: 1 / Fragment: UNP residues 152-193 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WVD5
#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 experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D CBCA(CO)NH
151isotropic13D C(CO)NH

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-13C; U-15N] RING finger protein 141, 90% H2O/10% D2O
Details: 20 mM Tris-d11-HCl buffer (pH 6.9) / Label: 15N 13C / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: RING finger protein 141 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 20 mM Tris-d11-HCl buffer / Ionic strength: 20 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
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
Discovery Studio2.1Accelrys Software Inc.structure calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichpeak picking
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: 100 / Conformers submitted total number: 20

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