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- PDB-2n3t: Solution structure of the Rpn1 substrate receptor site toroid 1 (T1) -

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Basic information

Entry
Database: PDB / ID: 2n3t
TitleSolution structure of the Rpn1 substrate receptor site toroid 1 (T1)
Components26S proteasome regulatory subunit RPN1
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / regulation of protein catabolic process / proteasome storage granule / Ub-specific processing proteases / enzyme regulator activity / Neutrophil degranulation / proteasome complex / protein-macromolecule adaptor activity ...proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / regulation of protein catabolic process / proteasome storage granule / Ub-specific processing proteases / enzyme regulator activity / Neutrophil degranulation / proteasome complex / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endoplasmic reticulum / nucleus / cytoplasm
Similarity search - Function
26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
26S proteasome regulatory subunit RPN1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, X. / Walters, K.J.
CitationJournal: Science / Year: 2016
Title: Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome.
Authors: Shi, Y. / Chen, X. / Elsasser, S. / Stocks, B.B. / Tian, G. / Lee, B.H. / Shi, Y. / Zhang, N. / de Poot, S.A. / Tuebing, F. / Sun, S. / Vannoy, J. / Tarasov, S.G. / Engen, J.R. / Finley, D. / Walters, K.J.
History
DepositionJun 10, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jun 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 1.3May 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 RPN1


Theoretical massNumber of molelcules
Total (without water)13,6371
Polymers13,6371
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 26S proteasome regulatory subunit RPN1 / HMG-CoA reductase degradation protein 2 / Proteasome non-ATPase subunit 1


Mass: 13636.592 Da / Num. of mol.: 1 / Fragment: UNP residues 482-612
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RPN1, HRD2, NAS1, RPD1, YHR027C / Plasmid: Pgex4t1 / Production host: Escherichia coli (E. coli) / References: UniProt: P38764

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1313D HN(CA)CB
1413D HNCA
1513D HN(CO)CA
1613D HNCO
1733D (H)CCH-TOCSY
1823D 1H-15N NOESY
1933D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 13C; U-100% 15N; U-80% 2H] protein, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.7 mM [U-100% 15N] protein, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.7 mM [U-100% 13C] protein, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMprotein-1[U-100% 13C; U-100% 15N; U-80% 2H]1
50 mMHEPES-21
50 mMsodium chloride-31
2 mMDTT-41
1 mMEDTA-51
0.1 %sodium azide-61
0.7 mMprotein-7[U-100% 15N]2
50 mMHEPES-82
50 mMsodium chloride-92
2 mMDTT-102
1 mMEDTA-112
0.1 %sodium azide-122
0.7 mMprotein-13[U-100% 13C]3
50 mMHEPES-143
50 mMsodium chloride-153
2 mMDTT-163
1 mMEDTA-173
0.1 %sodium azide-183
Sample conditionsIonic strength: 50 / pH: 6.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8501
Bruker AvanceBrukerAVANCE9002
Bruker AvanceBrukerAVANCE7003
Varian INOVAVarianINOVA8004

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
XEASYBartels et al.data analysis
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1242 / NOE intraresidue total count: 576 / NOE long range total count: 247 / NOE medium range total count: 241 / NOE sequential total count: 178 / Protein phi angle constraints total count: 91 / Protein psi angle constraints total count: 91
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 1.8 Å / Maximum upper distance constraint violation: 5.5 Å

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