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Yorodumi- PDB-6oa9: Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the... -
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-Basic information
Entry | Database: PDB / ID: 6oa9 | ||||||||||||
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Title | Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP | ||||||||||||
Components |
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Keywords | MOTOR PROTEIN / ATPase / ATPase complex / ubiquitin / quality control | ||||||||||||
Function / homology | Function and homology information SCF complex disassembly in response to cadmium stress / Ovarian tumor domain proteases / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / DNA replication termination / stress-induced homeostatically regulated protein degradation pathway / positive regulation of mitochondrial fusion / sister chromatid biorientation / ribophagy ...SCF complex disassembly in response to cadmium stress / Ovarian tumor domain proteases / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / DNA replication termination / stress-induced homeostatically regulated protein degradation pathway / positive regulation of mitochondrial fusion / sister chromatid biorientation / ribophagy / cytoplasm protein quality control by the ubiquitin-proteasome system / Hrd1p ubiquitin ligase ERAD-L complex / RQC complex / protein localization to vacuole / 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 / Translesion Synthesis by POLH / piecemeal microautophagy of the nucleus / mating projection tip / Protein methylation / vesicle-fusing ATPase / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / replisome / ribosome-associated ubiquitin-dependent protein catabolic process / nuclear outer membrane-endoplasmic reticulum membrane network / retrograde protein transport, ER to cytosol / KEAP1-NFE2L2 pathway / Neddylation / protein quality control for misfolded or incompletely synthesized proteins / autophagosome maturation / ribosomal large subunit export from nucleus / polyubiquitin modification-dependent protein binding / mRNA transport / ERAD pathway / ATP metabolic process / Neutrophil degranulation / rescue of stalled ribosome / ubiquitin binding / macroautophagy / ribosomal large subunit assembly / positive regulation of protein localization to nucleus / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / ubiquitin-dependent protein catabolic process / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Twomey, E.C. / Ji, Z. / Wales, T.E. / Bodnar, N.O. / Engen, J.R. / Rapoport, T.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Science / Year: 2019 Title: Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding. Authors: Edward C Twomey / Zhejian Ji / Thomas E Wales / Nicholas O Bodnar / Scott B Ficarro / Jarrod A Marto / John R Engen / Tom A Rapoport / Abstract: The Cdc48 adenosine triphosphatase (ATPase) (p97 or valosin-containing protein in mammals) and its cofactor Ufd1/Npl4 extract polyubiquitinated proteins from membranes or macromolecular complexes for ...The Cdc48 adenosine triphosphatase (ATPase) (p97 or valosin-containing protein in mammals) and its cofactor Ufd1/Npl4 extract polyubiquitinated proteins from membranes or macromolecular complexes for subsequent degradation by the proteasome. How Cdc48 processes its diverse and often well-folded substrates is unclear. Here, we report cryo-electron microscopy structures of the Cdc48 ATPase in complex with Ufd1/Npl4 and polyubiquitinated substrate. The structures show that the Cdc48 complex initiates substrate processing by unfolding a ubiquitin molecule. The unfolded ubiquitin molecule binds to Npl4 and projects its N-terminal segment through both hexameric ATPase rings. Pore loops of the second ring form a staircase that acts as a conveyer belt to move the polypeptide through the central pore. Inducing the unfolding of ubiquitin allows the Cdc48 ATPase complex to process a broad range of substrates. | ||||||||||||
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 | 6oa9.cif.gz | 672 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oa9.ent.gz | 534.7 KB | Display | PDB format |
PDBx/mmJSON format | 6oa9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oa9_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6oa9_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6oa9_validation.xml.gz | 108.2 KB | Display | |
Data in CIF | 6oa9_validation.cif.gz | 156.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/6oa9 ftp://data.pdbj.org/pub/pdb/validation_reports/oa/6oa9 | HTTPS FTP |
-Related structure data
Related structure data | 0665MC 0666C 6oaaC 6oabC 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 , 3 types, 10 molecules ABCDEFKHJG
#1: Protein | Mass: 92105.922 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CDC48, YDL126C / Production host: Escherichia coli (E. coli) / References: UniProt: P25694, vesicle-fusing ATPase #2: Protein | Mass: 8568.769 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPL40A, UBI1, YIL148W / Production host: Escherichia coli (E. coli) / References: UniProt: P0CH08 #3: Protein | | Mass: 65862.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NPL4, HRD4, YBR170C, YBR1231 / Production host: Escherichia coli (E. coli) / References: UniProt: P33755 |
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-Non-polymers , 3 types, 12 molecules
#4: Chemical | ChemComp-ATP / #5: Chemical | ChemComp-ADP / | #6: Chemical | |
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-Details
Has ligand of interest | N |
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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-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 295 K Details: Waited 20 seconds before blotting for 2.5-3 seconds. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 0 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 54.9 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127261 / Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 3.9 Å |