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- PDB-2z4d: NMR Structures of Yeast Proteasome Component Rpn13 -

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Basic information

Entry
Database: PDB / ID: 2z4d
TitleNMR Structures of Yeast Proteasome Component Rpn13
Components26S proteasome regulatory subunit RPN13
KeywordsNUCLEAR PROTEIN / Proteasome / PH domain
Function / homology
Function and homology information


proteasome regulatory particle, lid subcomplex / proteasome binding / proteasome storage granule / endopeptidase activator activity / proteasome complex / ubiquitin binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus
Similarity search - Function
Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / PH-domain like / Roll / Mainly Beta
Similarity search - Domain/homology
26S proteasome regulatory subunit RPN13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, N. / Walters, K.J.
CitationJournal: Nature / Year: 2008
Title: Proteasome subunit Rpn13 is a novel ubiquitin receptor.
Authors: Husnjak, K. / Elsasser, S. / Zhang, N. / Chen, X. / Randles, L. / Shi, Y. / Hofmann, K. / Walters, K.J. / Finley, D. / Dikic, I.
History
DepositionJun 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 26S proteasome regulatory subunit RPN13


Theoretical massNumber of molelcules
Total (without water)11,2211
Polymers11,2211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 35structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 26S proteasome regulatory subunit RPN13 / Proteasome Component Rpn13 / Proteasome non-ATPase subunit 13


Mass: 11220.795 Da / Num. of mol.: 1 / Fragment: residues 6-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPN13 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O13563

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB, HNCA/HN(CO)CA, HNCO/HN(CA)CO
1223D 15N-separated NOESY
1333D 13C-separated NOESY
143(H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM Rpn13 U-15N, 13C; U-70% 2H; 20mM phosphate buffer; 50mM NaCl; 4mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
20.5mM Rpn13 U-15N; U-50% 2H; 20mM phosphate buffer; 50mM NaCl; 4mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
30.5mM Rpn13 U-13C; 20mM phosphate buffer; 50mM NaCl; 4mM DTT; 100% D2O100% D2O
Sample conditionsIonic strength: 20mM phosphate, 50mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2006Frank Delaglio, Stephan Grzesiek, Guang Zhu, Geerten W. Vuister, John Pfeifer and Ad Baxprocessing
XEASY1996Tai-he Xia and Christian Bartelsdata analysis
X-PLOR3.851A. T. Brungerstructure solution
X-PLOR3.851refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1084 restraints, 949 are NOE-derived distance constraints, 79 dihedral angle restraints, 56 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 35 / Conformers submitted total number: 8

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