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Yorodumi- PDB-6omb: Cdc48 Hexamer (Subunits A to E) with substrate bound to the centr... -
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-Basic information
Entry | Database: PDB / ID: 6omb | ||||||
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Title | Cdc48 Hexamer (Subunits A to E) with substrate bound to the central pore | ||||||
Components |
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Keywords | MOTOR PROTEIN / Cdc48 / AAA+ ATPase / substrate translocation | ||||||
Function / homology | Function and homology information SCF complex disassembly in response to cadmium stress / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / ribophagy / DNA replication termination / Neddylation / stress-induced homeostatically regulated protein degradation pathway ...SCF complex disassembly in response to cadmium stress / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / ribophagy / DNA replication termination / Neddylation / stress-induced homeostatically regulated protein degradation pathway / positive regulation of mitochondrial fusion / sister chromatid biorientation / cytoplasm protein quality control by the ubiquitin-proteasome system / Hrd1p ubiquitin ligase ERAD-L complex / RQC complex / protein-containing complex disassembly / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / HSF1 activation / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / nonfunctional rRNA decay / protein phosphatase regulator activity / piecemeal microautophagy of the nucleus / mating projection tip / mitotic spindle disassembly / replisome / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / : / ribosome-associated ubiquitin-dependent protein catabolic process / retrograde protein transport, ER to cytosol / protein quality control for misfolded or incompletely synthesized proteins / autophagosome maturation / polyubiquitin modification-dependent protein binding / rescue of stalled ribosome / : / ATP metabolic process / Neutrophil degranulation / ubiquitin binding / macroautophagy / positive regulation of protein localization to nucleus / proteasome-mediated ubiquitin-dependent protein catabolic process / endoplasmic reticulum membrane / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Cooney, I. / Han, H. / Stewart, M. / Carson, R.H. / Hansen, D. / Price, J.C. / Hill, C.P. / Shen, P.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2019 Title: Structure of the Cdc48 segregase in the act of unfolding an authentic substrate. Authors: Ian Cooney / Han Han / Michael G Stewart / Richard H Carson / Daniel T Hansen / Janet H Iwasa / John C Price / Christopher P Hill / Peter S Shen / Abstract: The cellular machine Cdc48 functions in multiple biological pathways by segregating its protein substrates from a variety of stable environments such as organelles or multi-subunit complexes. Despite ...The cellular machine Cdc48 functions in multiple biological pathways by segregating its protein substrates from a variety of stable environments such as organelles or multi-subunit complexes. Despite extensive studies, the mechanism of Cdc48 has remained obscure, and its reported structures are inconsistent with models of substrate translocation proposed for other AAA+ ATPases (adenosine triphosphatases). Here, we report a 3.7-angstrom-resolution structure of Cdc48 in complex with an adaptor protein and a native substrate. Cdc48 engages substrate by adopting a helical configuration of substrate-binding residues that extends through the central pore of both of the ATPase rings. These findings indicate a unified hand-over-hand mechanism of protein translocation by Cdc48 and other AAA+ ATPases. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6omb.cif.gz | 499.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6omb.ent.gz | 400 KB | Display | PDB format |
PDBx/mmJSON format | 6omb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/6omb ftp://data.pdbj.org/pub/pdb/validation_reports/om/6omb | HTTPS FTP |
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-Related structure data
Related structure data | 20124MC 6opcC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 92106.914 Da / Num. of mol.: 5 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Variant: ATCC 204508 / S288c / Strain: ATCC 204508 / S288c / References: UniProt: P25694, vesicle-fusing ATPase #2: Protein/peptide | | Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) #3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-BEF / #5: Chemical | ChemComp-MG / |
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-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: Cdc48-Substrate Complex / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54367 / Symmetry type: POINT |
Refinement | Highest resolution: 3.7 Å |