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- EMDB-27278: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three u... -
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Open data
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Basic information
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Title | Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uD) | |||||||||
![]() | composite map of the ubiquitin unfolded state 'uD' | |||||||||
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Function / homology | ![]() SCF complex disassembly in response to cadmium stress / Josephin domain DUBs / RAS processing / Ovarian tumor domain proteases / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / endoplasmic reticulum membrane fusion / UCH proteinases / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Pexophagy ...SCF complex disassembly in response to cadmium stress / Josephin domain DUBs / RAS processing / Ovarian tumor domain proteases / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / endoplasmic reticulum membrane fusion / UCH proteinases / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Pexophagy / Interleukin-1 signaling / Aggrephagy / Doa10p ubiquitin ligase complex / DNA replication termination / stress-induced homeostatically regulated protein degradation pathway / positive regulation of mitochondrial fusion / sister chromatid biorientation / ribophagy / Peroxisomal protein import / cytoplasm protein quality control by the ubiquitin-proteasome system / Hrd1p ubiquitin ligase ERAD-L complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / 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 / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / HSF1 activation / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / E3 ubiquitin ligases ubiquitinate target proteins / nonfunctional rRNA decay / protein phosphatase regulator activity / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / piecemeal microautophagy of the nucleus / mating projection tip / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / 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 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / protein quality control for misfolded or incompletely synthesized proteins / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Gap-filling DNA repair synthesis and ligation in TC-NER / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / autophagosome maturation / Dual incision in TC-NER / polyubiquitin modification-dependent protein binding / mRNA transport / Ub-specific processing proteases / ERAD pathway / ATP metabolic process / Neutrophil degranulation / rescue of stalled ribosome / ubiquitin binding / macroautophagy / modification-dependent protein catabolic process / positive regulation of protein localization to nucleus / protein tag activity / ubiquitin-dependent protein catabolic process / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Lee HG / Lima CD | |||||||||
Funding support | ![]()
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![]() | ![]() Title: SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Authors: Hyein G Lee / Abigail A Lemmon / Christopher D Lima / ![]() Abstract: The Ufd1/Npl4/Cdc48 complex is a universal protein segregase that plays key roles in eukaryotic cellular processes. Its functions orchestrating the clearance or removal of polyubiquitylated targets ...The Ufd1/Npl4/Cdc48 complex is a universal protein segregase that plays key roles in eukaryotic cellular processes. Its functions orchestrating the clearance or removal of polyubiquitylated targets are established; however, prior studies suggest that the complex also targets substrates modified by the ubiquitin-like protein SUMO. Here, we show that interactions between Ufd1 and SUMO enhance unfolding of substrates modified by SUMO-polyubiquitin hybrid chains by the budding yeast Ufd1/Npl4/Cdc48 complex compared to substrates modified by polyubiquitin chains, a difference that is accentuated when the complex has a choice between these substrates. Incubating Ufd1/Npl4/Cdc48 with a substrate modified by a SUMO-polyubiquitin hybrid chain produced a series of single-particle cryo-EM structures that reveal features of interactions between Ufd1/Npl4/Cdc48 and ubiquitin prior to and during unfolding of ubiquitin. These results are consistent with cellular functions for SUMO and ubiquitin modifications and support a physical model wherein Ufd1/Npl4/Cdc48, SUMO, and ubiquitin conjugation pathways converge to promote clearance of proteins modified with SUMO and polyubiquitin. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 53.9 KB 53.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.6 KB | Display | ![]() |
Images | ![]() | 96 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 17.5 MB 9.9 MB 171.2 MB 171.2 MB 8 MB 13.5 MB 170.7 MB 170.7 MB 171.4 MB 171.2 MB 12.2 MB 171.2 MB 171.4 MB 171.5 MB 171.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 728.3 KB | Display | ![]() |
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Full document | ![]() | 727.9 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dawMC ![]() 8darC ![]() 8dasC ![]() 8datC ![]() 8dauC ![]() 8davC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | composite map of the ubiquitin unfolded state 'uD' | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
+Additional map: post-processed overall refinement map of the ubiquitin unfolded...
+Additional map: post-processed focused refinement map of the Ufd1/Npl4 tower...
+Additional map: focused refinement half map 1 of Cdc48 of...
+Additional map: focused refinement half map 1 of the Ufd1/Npl4...
+Additional map: post-processed focused refinement map of upper Ufd1/Npl4 tower...
+Additional map: post-processed focused refinement map of Cdc48 of the...
+Additional map: focused refinement half map 1 of upper Ufd1/Npl4...
+Additional map: focused refinement half map 2 of upper Ufd1/Npl4...
+Additional map: focused refinement half map 2 of the D1/D2...
+Additional map: focused refinement half map 2 of the Ufd1/Npl4...
+Additional map: post-processed focused refinement map of the D1/D2 ATPase...
+Additional map: focused refinement half map 2 of Cdc48 of...
+Additional map: focused refinement half map 1 of the D1/D2...
+Half map: overall refinement half map 2 of the ubiquitin unfolded state 'uD'
+Half map: overall refinement half map 1 of the ubiquitin unfolded state 'uD'
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Sample components
+Entire : Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three u...
+Supramolecule #1: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three u...
+Supramolecule #2: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three u...
+Supramolecule #3: Cdc48 hexamer
+Supramolecule #4: Three folded ubiqutin moieties and one unfolded ubiquitin bound t...
+Supramolecule #5: D1/D2 ATPase domains of the Cdc48 hexamer
+Supramolecule #6: Three folded Ubiqutin moieties bound to Npl4
+Macromolecule #1: Cell division control protein 48
+Macromolecule #2: Nuclear protein localization protein 4
+Macromolecule #3: Ubiquitin fusion degradation protein 1
+Macromolecule #4: Ubiquitin
+Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #7: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 Details: 20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 8 s wait, 4 s blot before plunging. |
Details | Ufd1/Npl4/Cdc48 was pre-incubated with SUMO-ubiquitin(K48polyUb)-mEOS and ATP |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.577 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |