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- PDB-6f98: Solution structure of the RING domain of the E3 ubiquitin ligase HRD1 -

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Basic information

Entry
Database: PDB / ID: 6f98
TitleSolution structure of the RING domain of the E3 ubiquitin ligase HRD1
ComponentsE3 ubiquitin-protein ligase
KeywordsLIGASE / RING domain / ubiquitin
Function / homology:
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKniss, A. / Kazemi, S. / Lohr, F. / Guntert, P. / Dotsch, V.
CitationJournal: To Be Published
Title: Solution structure of the RING domain of the E3 ubiquitin ligase HRD1
Authors: Kniss, A.
History
DepositionDec 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 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 1.3Jun 19, 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: E3 ubiquitin-protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1163
Polymers8,9851
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6600 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein E3 ubiquitin-protein ligase


Mass: 8985.388 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HRD1, SCKG_1066 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A250WAY8
#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
111isotropic43D 1H-15N NOESY
121isotropic43D 1H-13C NOESY aliphatic
131isotropic33D 1H-13C NOESY aromatic
141isotropic33D HN(CA)CB
171isotropic32D 1H-15N HSQC
161isotropic32D 1H-13C HSQC aliphatic
151isotropic32D 1H-13C HSQC aromatic
181isotropic33D 1H TOCSY
1101isotropic33D HNCO
191isotropic33D HN(CA)CO
1111isotropic33D HN(COCA)CB
1121isotropic32D HCBCGCDH TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-98% 13C; U-98% 15N] E3 ubiquitin ligase Hrd1, 95% H2O/5% D2O
Details: 25 mM HEPES, pH 7.0, 150 mM NaCl, 2 mM TCEP, protease inhibitor cocktail, NaN3, DSS, 5% D2O
Label: 13C_15N_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.8 mM / Component: E3 ubiquitin ligase Hrd1 / Isotopic labeling: [U-98% 13C; U-98% 15N]
Sample conditionsIonic strength: 150 mM / Label: condition_1 / pH: 7 / Pressure: AMBIENT bar / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7003
Bruker AVANCEBrukerAVANCE9504

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.13Goddardchemical shift assignment
CYANA3.9Peter Guntertstructure calculation
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Zinc included
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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