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- PDB-2ku1: Dynamic Regulation of Archaeal Proteasome Gate Opening as Studied... -

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Basic information

Entry
Database: PDB / ID: 2ku1
TitleDynamic Regulation of Archaeal Proteasome Gate Opening as Studied by TROSY-NMR
ComponentsProteasome subunit alpha
KeywordsHYDROLASE / proteasome / proteolysis / gating residues / Cytoplasm / Protease / Threonine protease
Function / homology
Function and homology information


proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / endopeptidase activity / cytoplasm
Similarity search - Function
Proteasome alpha subunit, archaeal / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit ...Proteasome alpha subunit, archaeal / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteasome subunit alpha
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsReliga, T.L. / Sprangers, R. / Kay, L.E.
CitationJournal: Science / Year: 2010
Title: Dynamic regulation of archaeal proteasome gate opening as studied by TROSY NMR.
Authors: Religa, T.L. / Sprangers, R. / Kay, L.E.
History
DepositionFeb 11, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha


Theoretical massNumber of molelcules
Total (without water)183,0217
Polymers183,0217
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)30 / 99structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein
Proteasome subunit alpha / / Multicatalytic endopeptidase complex subunit alpha


Mass: 26145.824 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmA, Ta1288 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Codon+ (RIPL)
References: UniProt: P25156, proteasome endopeptidase complex

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structures of N-terminal, gating residues, of proteasomal alpha subunit of T.acidophilum
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HMQC
1212D 1H-13C HMQC

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Sample preparation

DetailsContents: 0.2-3 mM [U-15N; U-2H; Met-1H,Met-CH3-13C] alpha-1, 100 % D2O-2, 25 mM potassium phosphate-3, 50 mM sodium chloride-4, 1 mM EDTA-5, 0.02 % sodium azide-6, 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMalpha-1[U-15N; U-2H; Met-1H,Met-CH3-13C]0.2-31
100 %D2O-21
25 mMpotassium phosphate-31
50 mMsodium chloride-41
1 mMEDTA-51
0.02 %sodium azide-61
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 323 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
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddarddata analysis
Sparky3.114Goddardpeak picking
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 99 / Conformers submitted total number: 30

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