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Yorodumi- PDB-3j47: Formation of an intricate helical bundle dictates the assembly of... -
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-Basic information
Entry | Database: PDB / ID: 3j47 | ||||||
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Title | Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid | ||||||
Components | (26S proteasome regulatory subunit ...) x 8 | ||||||
Keywords | PROTEIN BINDING / alpha helix bundle / hybrid method / flexible fitting | ||||||
Function / homology | Function and homology information Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / protein deneddylation / COP9 signalosome / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / mitochondrial fission / metal-dependent deubiquitinase activity / Cross-presentation of soluble exogenous antigens (endosomes) ...Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / protein deneddylation / COP9 signalosome / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / mitochondrial fission / metal-dependent deubiquitinase activity / 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 / KEAP1-NFE2L2 pathway / proteasome binding / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / regulation of protein catabolic process / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / proteasome assembly / Ub-specific processing proteases / 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 / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.4 Å | ||||||
Authors | Estrin, E. / Lopez-Blanco, J.R. / Chacon, P. / Martin, A. | ||||||
Citation | Journal: 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 |
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Remark 0 | THIS 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 |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j47.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j47.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 3j47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j47_validation.pdf.gz | 705.2 KB | Display | wwPDB validaton report |
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Full document | 3j47_full_validation.pdf.gz | 767.1 KB | Display | |
Data in XML | 3j47_validation.xml.gz | 28 KB | Display | |
Data in CIF | 3j47_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/3j47 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/3j47 | HTTPS FTP |
-Related structure data
Related structure data | 2165M M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-26S proteasome regulatory subunit ... , 8 types, 8 molecules VUOPQRST
#1: Protein | 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 |
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#2: Protein | 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 | 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 | 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 | 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 | 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 | 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 | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 26S proteasome / Type: COMPLEX |
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Buffer solution | pH: 7.1 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Mar 15, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 7.4 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 2464694 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: 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 step | Cycle: LAST
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