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- EMDB-20149: Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain) -

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Basic information

Entry
Database: EMDB / ID: EMD-20149
TitleCdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain)
Map data
SampleCdc48-Substrate Complex
  • Cell division control protein 48
  • Substrate bound to the central pore of the Cdc48 hexamer
  • UBX domain-containing protein 1
  • (ligand) x 3
Function / homology
Function and homology information


Ovarian tumor domain proteases / HSF1 activation / Translesion Synthesis by POLH / Neutrophil degranulation / SCF complex disassembly in response to cadmium stress / RQC complex / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / endoplasmic reticulum membrane fusion / nuclear envelope reassembly ...Ovarian tumor domain proteases / HSF1 activation / Translesion Synthesis by POLH / Neutrophil degranulation / SCF complex disassembly in response to cadmium stress / RQC complex / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / endoplasmic reticulum membrane fusion / nuclear envelope reassembly / ribophagy / cellular protein complex disassembly / stress-induced homeostatically regulated protein degradation pathway / ribosome-associated ubiquitin-dependent protein catabolic process / Hrd1p ubiquitin ligase ERAD-L complex / cytoplasm protein quality control by the ubiquitin-proteasome system / nuclear protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / sister chromatid biorientation / positive regulation of mitochondrial fusion / positive regulation of histone H2B ubiquitination / ascospore formation / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein phosphatase regulator activity / mitotic spindle disassembly / piecemeal microautophagy of the nucleus / ER-associated misfolded protein catabolic process / VCP-NPL4-UFD1 AAA ATPase complex / nonfunctional rRNA decay / vesicle-fusing ATPase / 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
ATPase, AAA-type, conserved site / Vps4 oligomerisation, C-terminal / CDC48, domain 2 / AAA ATPase, AAA+ lid domain / NSFL1 cofactor p47, SEP domain superfamily / Ubiquitin-like domain superfamily / CDC48 domain 2-like superfamily / P-loop containing nucleoside triphosphate hydrolase / SEP domain / Cell division protein 48 (CDC48), N-terminal domain ...ATPase, AAA-type, conserved site / Vps4 oligomerisation, C-terminal / CDC48, domain 2 / AAA ATPase, AAA+ lid domain / NSFL1 cofactor p47, SEP domain superfamily / Ubiquitin-like domain superfamily / CDC48 domain 2-like superfamily / P-loop containing nucleoside triphosphate hydrolase / SEP domain / Cell division protein 48 (CDC48), N-terminal domain / Aspartate decarboxylase-like domain superfamily / AAA ATPase, CDC48 family / UBX domain / CDC48, N-terminal subdomain / AAA+ ATPase domain / ATPase, AAA-type, core / UBX domain / ATPase family associated with various cellular activities (AAA) / UBX domain profile. / SEP domain profile. / Cell division protein 48 (CDC48), domain 2 / AAA-protein family signature. / SEP domain / AAA+ lid domain / Vps4 C terminal oligomerisation domain
Cell division control protein 48 / UBX domain-containing protein 1
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsCooney I / Han H / Stewart M / Carson RH / Hansen D / Price JC / Hill CP / Shen PS
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. Here, we report a 3.7 Å 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 ReportPDB-ID: 6opc

SummaryFull reportAbout validation report
DateDeposition: Apr 24, 2019 / Header (metadata) release: May 8, 2019 / Map release: Jul 10, 2019 / Update: Jul 10, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6opc
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20149.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 256 pix.
= 299.008 Å
1.17 Å/pix.
x 256 pix.
= 299.008 Å
1.17 Å/pix.
x 256 pix.
= 299.008 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.168 Å
Density
Contour LevelBy AUTHOR: 0.0056 / Movie #1: 0.008
Minimum - Maximum-0.027789509 - 0.06803693
Average (Standard dev.)0.000003440544 (±0.0025505817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 299.008 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1681.1681.168
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z299.008299.008299.008
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0280.0680.000

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Supplemental data

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Sample components

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Entire Cdc48-Substrate Complex

EntireName: Cdc48-Substrate Complex / Number of components: 7

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Component #1: protein, Cdc48-Substrate Complex

ProteinName: Cdc48-Substrate Complex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, Cell division control protein 48

ProteinName: Cell division control protein 48 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 92.106914 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #3: protein, Substrate bound to the central pore of the Cdc48 hexamer

ProteinName: Substrate bound to the central pore of the Cdc48 hexamer
Details: co-purified with Cdc48 hexamer / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.890321 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #4: protein, UBX domain-containing protein 1

ProteinName: UBX domain-containing protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.041105 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #5: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #6: ligand, BERYLLIUM TRIFLUORIDE ION

LigandName: BERYLLIUM TRIFLUORIDE ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 6.600705 MDa

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Component #7: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 54367
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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