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Basic information

Entry
Database: PDB / ID: 3j47
TitleFormation of an intricate helical bundle dictates the assembly of the 26S proteasome lid
Components(26S proteasome regulatory subunit ...) x 8
KeywordsPROTEIN BINDING / alpha helix bundle / hybrid method / flexible fitting
Function / homology
Function and homology information


Metalloprotease DUBs / proteasome storage granule assembly / protein deneddylation / peroxisome fission / COP9 signalosome / proteasome regulatory particle / mitochondrial fission / proteasome regulatory particle, lid subcomplex / metal-dependent deubiquitinase activity / Proteasome assembly ...Metalloprotease DUBs / proteasome storage granule assembly / protein deneddylation / peroxisome fission / COP9 signalosome / proteasome regulatory particle / mitochondrial fission / proteasome regulatory particle, lid subcomplex / metal-dependent deubiquitinase activity / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / proteasome binding / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / regulation of protein catabolic process / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / protein deubiquitination / Ub-specific processing proteases / proteasome assembly / enzyme regulator activity / Neutrophil degranulation / proteasome complex / metallopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / structural molecule activity / mitochondrion / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Rpn9, C-terminal helix / Rpn9 C-terminal helix / : / 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 / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / 26S proteasome regulatory subunit RPN5 C-terminal domain ...Rpn9, C-terminal helix / Rpn9 C-terminal helix / : / 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 / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / 26S proteasome regulatory subunit RPN5 C-terminal domain / PSD13 N-terminal repeats / 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 RPN11 C-terminal domain / : / : / : / PSMD12/CSN4, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 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 / Tetratricopeptide-like helical domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
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 (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsEstrin, E. / Lopez-Blanco, J.R. / Chacon, P. / Martin, A.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Near-atomic resolution structural model of the yeast 26S proteasome.
Authors: Florian Beck / Pia Unverdorben / Stefan Bohn / Andreas Schweitzer / Günter Pfeifer / Eri Sakata / Stephan Nickell / Jürgen M Plitzko / Elizabeth Villa / Wolfgang Baumeister / Friedrich Förster /
Abstract: The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or ...The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or 6.7 Å (Fourier-Shell Correlation of 0.5 or 0.3, respectively). We used this map in conjunction with molecular dynamics-based flexible fitting to build a near-atomic resolution model of the holocomplex. The quality of the map allowed us to assign α-helices, the predominant secondary structure element of the regulatory particle subunits, throughout the entire map. We were able to determine the architecture of the Rpn8/Rpn11 heterodimer, which had hitherto remained elusive. The MPN domain of Rpn11 is positioned directly above the AAA-ATPase N-ring suggesting that Rpn11 deubiquitylates substrates immediately following commitment and prior to their unfolding by the AAA-ATPase module. The MPN domain of Rpn11 dimerizes with that of Rpn8 and the C-termini of both subunits form long helices, which are integral parts of a coiled-coil module. Together with the C-terminal helices of the six PCI-domain subunits they form a very large coiled-coil bundle, which appears to serve as a flexible anchoring device for all the lid subunits.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Oct 2, 2013Group: Other
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0THIS ENTRY 3J47 CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-2165) DETERMINED ...THIS ENTRY 3J47 CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-2165) DETERMINED ORIGINALLY BY AUTHORS: F.BECK, P.UNVERDORBEN, S.BOHN, A.SCHWEITZER, G.PFEIFER, E.SAKATA, S.NICKELL, J.M.PLITZKO, E.VILLA, W.BAUMEISTER, F.FORSTER

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
V: 26S proteasome regulatory subunit RPN11
U: 26S proteasome regulatory subunit RPN8
O: 26S proteasome regulatory subunit RPN9
P: 26S proteasome regulatory subunit RPN5
Q: 26S proteasome regulatory subunit RPN6
R: 26S proteasome regulatory subunit RPN7
S: 26S proteasome regulatory subunit RPN3
T: 26S proteasome regulatory subunit RPN12


Theoretical massNumber of molelcules
Total (without water)39,8288
Polymers39,8288
Non-polymers00
Water00
1


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

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Components

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26S proteasome regulatory subunit ... , 8 types, 8 molecules VUOPQRST

#1: Protein 26S proteasome regulatory subunit RPN11 / Protein MPR1


Mass: 8013.857 Da / Num. of mol.: 1
Fragment: last three C-terminal helices (UNP residues 230-298)
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P43588
#2: Protein 26S proteasome regulatory subunit RPN8


Mass: 13965.031 Da / Num. of mol.: 1
Fragment: last three C-terminal helices (UNP residues 188-308)
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q08723
#3: Protein/peptide 26S proteasome regulatory subunit RPN9 / Proteasome non-ATPase subunit 7


Mass: 3353.889 Da / Num. of mol.: 1 / Fragment: C-terminal helix (UNP residues 360-387) / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q04062
#4: Protein/peptide 26S proteasome regulatory subunit RPN5 / Proteasome non-ATPase subunit 5


Mass: 3984.469 Da / Num. of mol.: 1 / Fragment: C-terminal helix (UNP residues 409-442) / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12250
#5: Protein/peptide 26S proteasome regulatory subunit RPN6 / Proteasome non-ATPase subunit 4


Mass: 2741.054 Da / Num. of mol.: 1 / Fragment: C-terminal helix (UNP residues 407-431) / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12377
#6: Protein/peptide 26S proteasome regulatory subunit RPN7


Mass: 2890.363 Da / Num. of mol.: 1 / Fragment: C-terminal helix (UNP residues 397-422) / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q06103
#7: Protein/peptide 26S proteasome regulatory subunit RPN3


Mass: 2924.156 Da / Num. of mol.: 1 / Fragment: C-terminal helix (UNP residues 455-478) / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40016
#8: Protein/peptide 26S proteasome regulatory subunit RPN12 / Nuclear integrity protein 1


Mass: 1955.234 Da / Num. of mol.: 1 / Fragment: C-terminal helix (UNP residues 256-272) / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32496

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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

ComponentName: 26S proteasome / Type: COMPLEX
Buffer solutionpH: 7.1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Mar 15, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMTEGRATORmodel fitting
2iMODFITmodel fitting
3VOLTRACmodel fitting
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.4 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 2464694 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--Hybrid method + flexible fitting REFINEMENT PROTOCOL--Hybrid method DETAILS--Initial model was done with an in house hybrid method (EMTEGRATOR) that integrates topology constraints ...Details: METHOD--Hybrid method + flexible fitting REFINEMENT PROTOCOL--Hybrid method DETAILS--Initial model was done with an in house hybrid method (EMTEGRATOR) that integrates topology constraints with EM-map derived constraints. iMODFIT was then used for final flexible fitting.
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 0 0 2498

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