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- PDB-6opc: Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain) -

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Basic information

Entry
Database: PDB / ID: 6opc
TitleCdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain)
Components
  • Cell division control protein 48
  • Substrate bound to the central pore of the Cdc48 hexamer
  • UBX domain-containing protein 1
KeywordsMOTOR PROTEIN / Cdc48 / AAA+ ATPase / substrate translocation
Function / homology
Function and homology information


SCF complex disassembly in response to cadmium stress / endoplasmic reticulum membrane fusion / Doa10p ubiquitin ligase complex / RQC complex / cellular protein complex disassembly / Cdc48p-Npl4p-Vms1p AAA ATPase complex / stress-induced homeostatically regulated protein degradation pathway / nuclear envelope reassembly / ribophagy / ribosome-associated ubiquitin-dependent protein catabolic process ...SCF complex disassembly in response to cadmium stress / endoplasmic reticulum membrane fusion / Doa10p ubiquitin ligase complex / RQC complex / cellular protein complex disassembly / Cdc48p-Npl4p-Vms1p AAA ATPase complex / stress-induced homeostatically regulated protein degradation pathway / nuclear envelope reassembly / ribophagy / ribosome-associated ubiquitin-dependent protein catabolic process / DNA replication termination / sister chromatid biorientation / nuclear protein quality control by the ubiquitin-proteasome system / cytoplasm protein quality control by the ubiquitin-proteasome system / ascospore formation / mitochondria-associated ubiquitin-dependent protein catabolic process / positive regulation of mitochondrial fusion / Hrd1p ubiquitin ligase ERAD-L complex / positive regulation of histone H2B ubiquitination / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / replisome / protein phosphatase regulator activity / piecemeal microautophagy of the nucleus / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / ER-associated misfolded protein catabolic process / vesicle-fusing ATPase / nonfunctional rRNA decay / retrograde protein transport, ER to cytosol / membrane fusion / mating projection tip / autophagosome maturation / Golgi organization / ATP metabolic process / autophagosome assembly / polyubiquitin modification-dependent protein binding / glycogen metabolic process / ubiquitin-dependent ERAD pathway / negative regulation of telomerase activity / ubiquitin binding / macroautophagy / positive regulation of protein localization to nucleus / proteasome-mediated ubiquitin-dependent protein catabolic process / ATPase activity / endoplasmic reticulum membrane / mitochondrion / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
UBA-like domain / Ubiquitin-like domain superfamily / UBX domain / CDC48, N-terminal subdomain / AAA+ ATPase domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / CDC48, domain 2 / AAA ATPase, CDC48 family / Aspartate decarboxylase-like domain superfamily ...UBA-like domain / Ubiquitin-like domain superfamily / UBX domain / CDC48, N-terminal subdomain / AAA+ ATPase domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / CDC48, domain 2 / AAA ATPase, CDC48 family / Aspartate decarboxylase-like domain superfamily / SEP domain / P-loop containing nucleoside triphosphate hydrolase / CDC48 domain 2-like superfamily / Vps4 oligomerisation, C-terminal / NSFL1 cofactor p47, SEP domain superfamily / ATPase family associated with various cellular activities (AAA) / SEP domain / UBX domain / AAA+ lid domain / Vps4 C terminal oligomerisation domain / Cell division protein 48 (CDC48), N-terminal domain / Cell division protein 48 (CDC48), domain 2 / AAA ATPase, AAA+ lid domain
Cell division control protein 48 / UBX domain-containing protein 1
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsCooney, I. / Han, H. / Stewart, M. / Carson, R.H. / Hansen, D. / Price, J.C. / Hill, C.P. / Shen, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P50GM082545 United States
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: Cell division control protein 48
B: Cell division control protein 48
C: Cell division control protein 48
D: Cell division control protein 48
E: Cell division control protein 48
F: Cell division control protein 48
G: Substrate bound to the central pore of the Cdc48 hexamer
Z: UBX domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)606,56734
Polymers601,5738
Non-polymers4,99526
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Limited by our current resolution for the N domain and Shp1, we can only observe one Shp1 binding to the Cdc48 hexamer.
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 7 molecules ABCDEFZ

#1: Protein
Cell division control protein 48 / Cell division cycle protein 48 / Transitional endoplasmic reticulum ATPase homolog / Cdc48


Mass: 92106.914 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P25694, vesicle-fusing ATPase
#3: Protein UBX domain-containing protein 1 / Suppressor of high-copy PP1 protein / Shp1


Mass: 47041.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P34223

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Protein/peptide , 1 types, 1 molecules G

#2: Protein/peptide Substrate bound to the central pore of the Cdc48 hexamer


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 (baker's yeast)

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Non-polymers , 3 types, 26 molecules

#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: BeF3
#6: Chemical
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg

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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: Cdc48-Substrate Complex / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54367 / Symmetry type: POINT

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