+Open data
-Basic information
Entry | Database: PDB / ID: 6opc | ||||||
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Title | Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain) | ||||||
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 / mitotic DNA replication termination / Ovarian tumor domain proteases / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / stress-induced homeostatically regulated protein degradation pathway / Hrd1p ubiquitin ligase ERAD-L complex / sister chromatid biorientation / DNA replication termination ...SCF complex disassembly in response to cadmium stress / mitotic DNA replication termination / Ovarian tumor domain proteases / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / stress-induced homeostatically regulated protein degradation pathway / Hrd1p ubiquitin ligase ERAD-L complex / sister chromatid biorientation / DNA replication termination / ribophagy / ascospore formation / RQC complex / mitochondria-associated ubiquitin-dependent protein catabolic process / protein-containing complex disassembly / cytoplasm protein quality control by the ubiquitin-proteasome system / positive regulation of mitochondrial fusion / HSF1 activation / nuclear protein quality control by the ubiquitin-proteasome system / endosome to plasma membrane protein transport / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / nuclear membrane reassembly / protein phosphatase regulator activity / Translesion Synthesis by POLH / piecemeal microautophagy of the nucleus / mating projection tip / replisome / Protein methylation / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / ribosome-associated ubiquitin-dependent protein catabolic process / nonfunctional rRNA decay / retrograde protein transport, ER to cytosol / K48-linked polyubiquitin modification-dependent protein binding / glycogen metabolic process / KEAP1-NFE2L2 pathway / protein quality control for misfolded or incompletely synthesized proteins / Neddylation / Golgi organization / polyubiquitin modification-dependent protein binding / autophagosome maturation / autophagosome assembly / ATP metabolic process / ERAD pathway / Neutrophil degranulation / rescue of stalled ribosome / ubiquitin binding / macroautophagy / positive regulation of protein localization to nucleus / proteasome-mediated ubiquitin-dependent protein catabolic process / membrane fusion / endoplasmic reticulum membrane / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's 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 | 6opc.cif.gz | 728.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6opc.ent.gz | 565.1 KB | Display | PDB format |
PDBx/mmJSON format | 6opc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6opc_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6opc_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6opc_validation.xml.gz | 103.1 KB | Display | |
Data in CIF | 6opc_validation.cif.gz | 166.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/6opc ftp://data.pdbj.org/pub/pdb/validation_reports/op/6opc | HTTPS FTP |
-Related structure data
Related structure data | 20149MC 6ombC 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
-Protein , 2 types, 7 molecules ABCDEFZ
#1: Protein | Mass: 92106.914 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25694, vesicle-fusing ATPase #3: Protein | | Mass: 47041.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34223 |
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-Protein/peptide , 1 types, 1 molecules G
#2: Protein/peptide | Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: co-purified with Cdc48 hexamer / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
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-Non-polymers , 3 types, 26 molecules
#4: Chemical | ChemComp-ADP / #5: Chemical | ChemComp-BEF / #6: 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-#3 / Source: NATURAL |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
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 FIELD |
Image recording | Electron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54367 / Symmetry type: POINT |