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- PDB-5zmr: Solution Structure of the N-terminal Domain of the Yeast Rpn5 -

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Basic information

Entry
Database: PDB / ID: 5zmr
TitleSolution Structure of the N-terminal Domain of the Yeast Rpn5
Components26S proteasome regulatory subunit RPN5
KeywordsHYDROLASE / a-helix bundle
Function / homology
Function and homology information


protein deneddylation / COP9 signalosome / proteasome regulatory particle, lid subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway ...protein deneddylation / COP9 signalosome / proteasome regulatory particle, lid subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / Neutrophil degranulation / proteasome complex / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoplasm
Similarity search - Function
26S proteasome regulatory subunit RPN5, C-terminal domain / 26S proteasome regulatory subunit RPN5 C-terminal domain / PSMD12/CSN4, N-terminal / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
26S proteasome regulatory subunit RPN5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, W. / Zhao, C. / Li, H. / Hu, Y. / Jin, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570757 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Solution structure of the N-terminal domain of proteasome lid subunit Rpn5
Authors: Zhang, W. / Zhao, C. / Hu, Y. / Jin, C.
History
DepositionApr 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _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: 26S proteasome regulatory subunit RPN5


Theoretical massNumber of molelcules
Total (without water)15,6181
Polymers15,6181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9140 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 26S proteasome regulatory subunit RPN5 / Proteasome non-ATPase subunit 5


Mass: 15618.022 Da / Num. of mol.: 1 / Fragment: N terminal domain, residues 1-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPN5, NAS5, YDL147W, D1572 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12250

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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
121isotropic12D 1H-13C HSQC
131isotropic13D HNCA
141isotropic13D HN(CO)CA
151isotropic13D HNCO
171isotropic13D HN(CA)CO
161isotropic13D HN(CA)CB
181isotropic13D CBCA(CO)NH
1101isotropic13D HBHA(CO)NH
191isotropic13D (H)CCH-COSY
1111isotropic13D (H)CCH-COSY
1121isotropic13D 15N-edited TOCSY-HSQC
1131isotropic23D 1H-15N NOESY
1141isotropic23D 1H-15C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.3 mM [U-95% 13C; U-95% 15N] 26S proteasome regulatory subunit Rpn5, 10 % v/v [U-99% 2H] D2O, 0.1 mg/mL DSS, 1 mM DTT, 50 mM sodium phosphate, 50 mM sodium sulfate, 2 % v/v ...Contents: 0.3 mM [U-95% 13C; U-95% 15N] 26S proteasome regulatory subunit Rpn5, 10 % v/v [U-99% 2H] D2O, 0.1 mg/mL DSS, 1 mM DTT, 50 mM sodium phosphate, 50 mM sodium sulfate, 2 % v/v trifluoroethanol, 5 % w/v sucrose, 90% H2O/10% D2O
Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mM26S proteasome regulatory subunit Rpn5[U-95% 13C; U-95% 15N]1
10 % v/vD2O[U-99% 2H]1
0.1 mg/mLDSSnatural abundance1
1 mMDTTnatural abundance1
50 mMsodium phosphatenatural abundance1
50 mMsodium sulfatenatural abundance1
2 % v/vtrifluoroethanolnatural abundance1
5 % w/vsucrosenatural abundance1
Sample conditionsIonic strength: 50 mM sodium phosphate buffer, 50 mM Na2SO4 mM
Label: condition_1 / pH: 6 / Pressure: ambient Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III5001
Bruker AVANCE IIIBrukerAVANCE III9502

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Processing

NMR software
NameVersionDeveloperClassification
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRView5.0.4Johnson, One Moon Scientificchemical shift assignment
NMRView5.0.4Johnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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