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- PDB-3jck: Structure of the yeast 26S proteasome lid sub-complex -

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Basic information

Entry
Database: PDB / ID: 3jck
TitleStructure of the yeast 26S proteasome lid sub-complex
Components
  • (26S proteasome regulatory subunit ...) x 7
  • 26S proteasome complex subunit SEM1Proteasome
  • Ubiquitin carboxyl-terminal hydrolase RPN11
KeywordsHYDROLASE / Proteasome / deubiquitinase / Rpn11 / protein homeostasis
Function / homology
Function and homology information


SAGA complex localization to transcription regulatory region / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex ...SAGA complex localization to transcription regulatory region / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / mitochondrial fission / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / proteasome binding / regulation of protein catabolic process / protein deubiquitination / proteasome storage granule / proteasome assembly / enzyme regulator activity / mRNA export from nucleus / protein folding chaperone / Neutrophil degranulation / proteasome complex / double-strand break repair via homologous recombination / metallopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / regulation of cell cycle / structural molecule activity / positive regulation of transcription by RNA polymerase II / mitochondrion / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #570 / Rpn9, C-terminal helix / Rpn9 C-terminal helix / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #570 / Rpn9, C-terminal helix / Rpn9 C-terminal helix / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / DSS1/SEM1 / 26S proteasome regulatory subunit RPN5, C-terminal domain / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN5 C-terminal domain / DSS1_SEM1 / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 13 / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / PCI/PINT associated module / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / TPR repeat region circular profile. / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / TPR repeat profile. / MPN domain / MPN domain profile. / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
26S proteasome complex subunit SEM1 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit RPN3 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit RPN6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHerzik Jr., M.A. / Dambacher, C.M. / Worden, E.J. / Martin, A. / Lander, G.C.
CitationJournal: Elife / Year: 2016
Title: Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition.
Authors: Corey M Dambacher / Evan J Worden / Mark A Herzik / Andreas Martin / Gabriel C Lander /
Abstract: The 26S proteasome is responsible for the selective, ATP-dependent degradation of polyubiquitinated cellular proteins. Removal of ubiquitin chains from targeted substrates at the proteasome is a ...The 26S proteasome is responsible for the selective, ATP-dependent degradation of polyubiquitinated cellular proteins. Removal of ubiquitin chains from targeted substrates at the proteasome is a prerequisite for substrate processing and is accomplished by Rpn11, a deubiquitinase within the 'lid' sub-complex. Prior to the lid's incorporation into the proteasome, Rpn11 deubiquitinase activity is inhibited to prevent unwarranted deubiquitination of polyubiquitinated proteins. Here we present the atomic model of the isolated lid sub-complex, as determined by cryo-electron microscopy at 3.5 Å resolution, revealing how Rpn11 is inhibited through its interaction with a neighboring lid subunit, Rpn5. Through mutagenesis of specific residues, we describe the network of interactions that are required to stabilize this inhibited state. These results provide significant insight into the intricate mechanisms of proteasome assembly, outlining the substantial conformational rearrangements that occur during incorporation of the lid into the 26S holoenzyme, which ultimately activates the deubiquitinase for substrate degradation.
History
DepositionDec 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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Assembly

Deposited unit
A: 26S proteasome regulatory subunit RPN3
B: 26S proteasome regulatory subunit RPN5
C: 26S proteasome regulatory subunit RPN6
D: 26S proteasome regulatory subunit RPN7
E: 26S proteasome regulatory subunit RPN8
F: 26S proteasome regulatory subunit RPN9
G: Ubiquitin carboxyl-terminal hydrolase RPN11
H: 26S proteasome regulatory subunit RPN12
I: 26S proteasome complex subunit SEM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,33210
Polymers361,2679
Non-polymers651
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Number of models5

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Components

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26S proteasome regulatory subunit ... , 7 types, 7 molecules ABCDEFH

#1: Protein 26S proteasome regulatory subunit RPN3


Mass: 49573.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Cellular location: cytoplasm / Gene: RPN3, SUN2, YER021W / Plasmid: pET, pCOLA, pACYC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40016
#2: Protein 26S proteasome regulatory subunit RPN5 / Proteasome non-ATPase subunit 5


Mass: 51840.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Cellular location: cytoplasm / Gene: RPN5, NAS5, YDL147W, D1572 / Plasmid: pET, pCOLA, pACYC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12250
#3: Protein 26S proteasome regulatory subunit RPN6 / Proteasome non-ATPase subunit 4


Mass: 49839.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Cellular location: cytoplasm / Gene: RPN6, NAS4, YDL097C, D2381 / Plasmid: pET, pCOLA, pACYC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12377
#4: Protein 26S proteasome regulatory subunit RPN7


Mass: 49016.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Cellular location: cytoplasm / Gene: RPN7, YPR108W, P8283.8 / Plasmid: pET, pCOLA, pACYC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06103
#5: Protein 26S proteasome regulatory subunit RPN8


Mass: 38365.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Cellular location: cytoplasm / Gene: RPN8, YOR261C, O5360 / Plasmid: pET, pCOLA, pACYC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08723
#6: Protein 26S proteasome regulatory subunit RPN9 / Proteasome non-ATPase subunit 7


Mass: 45839.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Cellular location: cytoplasm / Gene: RPN9, NAS7, YDR427W, D9461.14 / Plasmid: pET, pCOLA, pACYC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04062
#8: Protein 26S proteasome regulatory subunit RPN12 / Nuclear integrity protein 1


Mass: 31952.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Cellular location: cytoplasm / Gene: RPN12, NIN1, YFR052W / Plasmid: pET, pCOLA, pACYC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32496

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Protein , 2 types, 2 molecules GI

#7: Protein Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN11 / Protein MPR1


Mass: 34442.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Cellular location: cytoplasm / Gene: RPN11, MPR1, YFR004W / Plasmid: pET, pCOLA, pACYC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P43588, ubiquitinyl hydrolase 1
#9: Protein 26S proteasome complex subunit SEM1 / Proteasome


Mass: 10397.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Cellular location: cytoplasm / Gene: SEM1, DSH1, YDR363W-A / Plasmid: pET, pCOLA, pACYC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94742

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Non-polymers , 2 types, 2 molecules

#10: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsParent-ID
1Recombinant yeast 26S proteasome lid complexCOMPLEX9 subunits0
226S proteasome lid sub-complex1
Molecular weightValue: 0.37 MDa / Experimental value: YES
Buffer solutionName: 50 mM HEPES, 100 mM NaCl, 100 mM KCl, 1 mM TCEP / pH: 7.5 / Details: 50 mM HEPES, 100 mM NaCl, 100 mM KCl, 1 mM TCEP
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Sample was applied directly to plasma-cleaned holey carbon C-flat grids (400 mesh, 1.2 micrometer holes).
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 85 K / Humidity: 88 %
Details: 4 uL sample was applied to the grid, blotted for 2 seconds at 4 degrees C, and plunged into liquid ethane using a manual plunger.
Method: 4 uL sample was applied to the grid, blotted for 2 seconds, and plunged into liquid ethane.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Feb 10, 2015
Details: Micrograph was collected in super-resolution mode with a total frame count of 38 and total exposure time of 7.6 seconds.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Calibrated magnification: 38168 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm
Astigmatism: Objective lens astigmatism was corrected at a nominal magnification of 22,500.
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 87.5 K / Temperature (max): 90 K / Temperature (min): 85 K
Image recordingElectron dose: 43.8 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNum. digital images: 3432

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Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2FindEMparticle selection
3Appion3D reconstruction
4RELION3D reconstruction
CTF correctionDetails: whole micrograph
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: projection matching / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109396 / Nominal pixel size: 1.31 Å / Actual pixel size: 1.31 Å
Details: 3D classification was performed to identify the best 109,396 particles from an initial dataset of 254,112. An ensemble of five models is provided. Each model is an approximately equivalent ...Details: 3D classification was performed to identify the best 109,396 particles from an initial dataset of 254,112. An ensemble of five models is provided. Each model is an approximately equivalent representation of the structure. (Single particle details: Image pre-processing was performed using Appion. 3D classification and reconstruction was performed with RELION.) (Single particle--Applied symmetry: C1)
Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms22455 0 1 1 22457

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