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- PDB-2kr0: Solution structure of the proteasome ubiquitin receptor Rpn13 -

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Basic information

Entry
Database: PDB / ID: 2kr0
TitleSolution structure of the proteasome ubiquitin receptor Rpn13
ComponentsProteasomal ubiquitin receptor ADRM1
KeywordsPROTEIN BINDING / Proteasome / ubiquitin / 19S regulator
Function / homology
Function and homology information


proteasome regulatory particle, lid subcomplex / molecular function inhibitor activity / proteasome binding / endopeptidase activator activity / proteasome assembly / proteasome complex / transcription elongation by RNA polymerase II / UCH proteinases / protease binding / proteasome-mediated ubiquitin-dependent protein catabolic process ...proteasome regulatory particle, lid subcomplex / molecular function inhibitor activity / proteasome binding / endopeptidase activator activity / proteasome assembly / proteasome complex / transcription elongation by RNA polymerase II / UCH proteinases / protease binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
uronate isomerase, domain 2, chain A - #20 / Proteasomal ubiquitin receptor Rpn13/ADRM1 / uronate isomerase, domain 2, chain A / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily ...uronate isomerase, domain 2, chain A - #20 / Proteasomal ubiquitin receptor Rpn13/ADRM1 / uronate isomerase, domain 2, chain A / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Proteasomal ubiquitin receptor ADRM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsChen, X. / Lee, B. / Finley, D. / Walters, K.J.
CitationJournal: Mol.Cell / Year: 2010
Title: Structure of Proteasome Ubiquitin Receptor hRpn13 and Its Activation by the Scaffolding Protein hRpn2.
Authors: Chen, X. / Lee, B.H. / Finley, D. / Walters, K.J.
History
DepositionNov 25, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 23, 2015Group: Structure summary
Revision 1.3Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasomal ubiquitin receptor ADRM1


Theoretical massNumber of molelcules
Total (without water)42,4851
Polymers42,4851
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)31 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Proteasomal ubiquitin receptor ADRM1 / Adhesion-regulating molecule 1 / ARM-1 / 110 kDa cell membrane glycoprotein / Gp110 / Rpn13 homolog ...Adhesion-regulating molecule 1 / ARM-1 / 110 kDa cell membrane glycoprotein / Gp110 / Rpn13 homolog / Proteasome regulatory particle non-ATPase 13 / hRpn13


Mass: 42485.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRM1, GP110 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: Q16186

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1312D 1H-15N HSQC
NMR detailsText: The Spectra took in Bruker Advance 700 MHz are a set of spin-labeling experiments to achieve PRE data.

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Sample preparation

DetailsContents: 0.1 mM [U-15N] protein, 0.1 mM [U-15N; U-50% 2H] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMprotein-1[U-15N]1
0.1 mMprotein-2[U-15N; U-50% 2H]1
Sample conditionsIonic strength: 20 mM phosphate, 50 mM NaCl / pH: 6.5 / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002
Bruker AvanceBrukerAVANCE7003

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
TopSpinBruker Biospincollection
NMRPipe2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASY6.4Bartels et al.chemical shift assignment
XEASY6.4Bartels et al.data analysis
XEASY6.4Bartels et al.peak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure of two functional domain of the protein is calculated based on their NOE-derived distance constraints, hydrogen bonds and dihedral angle restraints. The paramagnetic relaxation ...Details: The structure of two functional domain of the protein is calculated based on their NOE-derived distance constraints, hydrogen bonds and dihedral angle restraints. The paramagnetic relaxation enhancement from spin-labeling experiments and inter-domain NOE help define the structure of full protein.
NMR constraintsNOE constraints total: 4948 / Hydrogen bond constraints total count: 234
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 31

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