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Yorodumi- EMDB-27276: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two fol... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27276 | |||||||||
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Title | Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two folded ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (uA) | |||||||||
Map data | composite map of the ubiquitin unfolded state 'uA' | |||||||||
Sample |
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Function / homology | Function and homology information SCF complex disassembly in response to cadmium stress / Josephin domain DUBs / RAS processing / mitotic DNA replication termination / PINK1-PRKN Mediated Mitophagy / Ovarian tumor domain proteases / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / endoplasmic reticulum membrane fusion ...SCF complex disassembly in response to cadmium stress / Josephin domain DUBs / RAS processing / mitotic DNA replication termination / PINK1-PRKN Mediated Mitophagy / Ovarian tumor domain proteases / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Pexophagy / Interleukin-1 signaling / Aggrephagy / Doa10p ubiquitin ligase complex / Regulation of pyruvate metabolism / stress-induced homeostatically regulated protein degradation pathway / Hrd1p ubiquitin ligase ERAD-L complex / sister chromatid biorientation / DNA replication termination / Peroxisomal protein import / ribophagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / RQC complex / protein localization to vacuole / 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 / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / 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 / E3 ubiquitin ligases ubiquitinate target proteins / protein phosphatase regulator activity / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / piecemeal microautophagy of the nucleus / mating projection tip / replisome / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / 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 / nuclear outer membrane-endoplasmic reticulum membrane network / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / protein quality control for misfolded or incompletely synthesized proteins / 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 / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / polyubiquitin modification-dependent protein binding / autophagosome maturation / Dual incision in TC-NER / mRNA transport / Ub-specific processing proteases / ATP metabolic process / ERAD pathway / Neutrophil degranulation / rescue of stalled ribosome / ubiquitin binding / macroautophagy / positive regulation of protein localization to nucleus / modification-dependent protein catabolic process / protein tag activity / peroxisome / 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 Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Lee HG / Lima CD | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 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 | emd_27276.map.gz | 32.6 MB | EMDB map data format | |
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Header (meta data) | emd-27276-v30.xml emd-27276.xml | 54.1 KB 54.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27276_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_27276.png | 88.6 KB | ||
Others | emd_27276_additional_1.map.gz emd_27276_additional_10.map.gz emd_27276_additional_11.map.gz emd_27276_additional_12.map.gz emd_27276_additional_13.map.gz emd_27276_additional_2.map.gz emd_27276_additional_3.map.gz emd_27276_additional_4.map.gz emd_27276_additional_5.map.gz emd_27276_additional_6.map.gz emd_27276_additional_7.map.gz emd_27276_additional_8.map.gz emd_27276_additional_9.map.gz emd_27276_half_map_1.map.gz emd_27276_half_map_2.map.gz | 17.5 MB 13.4 MB 171.5 MB 9.7 MB 171.1 MB 171.3 MB 171.3 MB 171.1 MB 171 MB 171.5 MB 171 MB 12.7 MB 10.2 MB 171.5 MB 171.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27276 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27276 | HTTPS FTP |
-Validation report
Summary document | emd_27276_validation.pdf.gz | 722.4 KB | Display | EMDB validaton report |
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Full document | emd_27276_full_validation.pdf.gz | 722 KB | Display | |
Data in XML | emd_27276_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | emd_27276_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27276 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27276 | HTTPS FTP |
-Related structure data
Related structure data | 8dauMC 8darC 8dasC 8datC 8davC 8dawC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27276.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | composite map of the ubiquitin unfolded state 'uA' | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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: overall refinement post-processed map of the ubiquitin unfolded...
+Additional map: post-processed focused refinement map of the D1/D2 domains...
+Additional map: focused refinement half map 1 of Cdc48 of...
+Additional map: post-processed focused refinement map of Npl4 and polyubiquitin...
+Additional map: focused refinement half map 1 of Npl4 and...
+Additional map: focused refinement half map 2 of the D1/D2...
+Additional map: focused refinement half map 1 of the D1/D2...
+Additional map: focused refinement half map 1 of the central...
+Additional map: focused refinement half map 2 of Npl4/polyubiquitin density...
+Additional map: focused refinement half map 2 of Cdc48 of...
+Additional map: focused refinement half map 2 of the central...
+Additional map: post-processed focused refinement map of Cdc48 of the...
+Additional map: post-processed focused refinement map of the central Ufd1/Npl4/polyubiquitin...
+Half map: overall refinement half map 1
+Half map: overall refinement half map 2 of the ubiquitin unfolded state 'uA'
-Sample components
+Entire : Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two Ubi...
+Supramolecule #1: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two Ubi...
+Supramolecule #2: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubi...
+Supramolecule #3: Cdc48 hexamer
+Supramolecule #4: Two folded ubiqutin moieties and one unfolded ubiquitin bound to ...
+Supramolecule #5: D1/D2 ATPase domains of the Cdc48 hexamer
+Supramolecule #6: Two 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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Processing | single particle reconstruction |
Aggregation state | particle |
-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. |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
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 |
-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: FIELD EMISSION GUN |
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 |