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- PDB-8dau: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two fol... -
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Basic information
Entry | Database: PDB / ID: 8dau | |||||||||
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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) | |||||||||
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![]() | MOTOR PROTEIN / ATPASE / ATPASE COMPLEX / UBIQUITIN / SUMO / SMT3 / QUALITY CONTROL | |||||||||
Function / homology | ![]() SCF complex disassembly in response to cadmium stress / Josephin domain DUBs / RAS processing / mitotic DNA replication termination / 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 ...SCF complex disassembly in response to cadmium stress / Josephin domain DUBs / RAS processing / mitotic DNA replication termination / 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 / Regulation of pyruvate metabolism / DNA replication termination / stress-induced homeostatically regulated protein degradation pathway / Hrd1p ubiquitin ligase ERAD-L complex / sister chromatid biorientation / Peroxisomal protein import / ribophagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / RQC complex / protein localization to vacuole / protein-containing complex disassembly / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / positive regulation of mitochondrial fusion / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / 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 / E3 ubiquitin ligases ubiquitinate target proteins / endosome to plasma membrane protein transport / 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 / replisome / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / ribosome-associated ubiquitin-dependent protein catabolic process / nonfunctional rRNA decay / K48-linked polyubiquitin modification-dependent protein binding / 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 / protein quality control for misfolded or incompletely synthesized proteins / 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 / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / 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 / positive regulation of protein localization to nucleus / modification-dependent protein catabolic process / protein tag activity / peroxisome / nuclear membrane / ubiquitin-dependent protein catabolic process / 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 Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Lee, H.G. / Lima, C.D. | |||||||||
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. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 771 KB | Display | ![]() |
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PDB format | ![]() | 622.8 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 27276MC ![]() 8darC ![]() 8dasC ![]() 8datC ![]() 8davC ![]() 8dawC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 11 molecules ABCDEFGHIJK
#1: Protein | Mass: 92389.195 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CDC48, YDL126C / Production host: ![]() ![]() #2: Protein | | Mass: 66144.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: NPL4, HRD4, YBR170C, YBR1231 / Production host: ![]() ![]() #3: Protein | | Mass: 40001.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: UFD1, PIP3, YGR048W / Production host: ![]() ![]() #4: Protein | Mass: 8568.769 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: ubiquitin that is part of the SUMO-ubiquitin(K48polyUb)-mEOS substrate; SUMO-ubiquitin-mEOS modified on K48 of Ub with a K48-linked polyubiquitin. Sequence of the unmodified substrate is ...Details: ubiquitin that is part of the SUMO-ubiquitin(K48polyUb)-mEOS substrate; SUMO-ubiquitin-mEOS modified on K48 of Ub with a K48-linked polyubiquitin. Sequence of the unmodified substrate is MGSSHHHHHHSSGENLYFQGHMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSHMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMSAIKPDMKIKLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAKYPDNIQDYFKQSFPKGYSWERSLTFEDGGICNARNDITMEGDTFYNKVRFYGTNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDIEMALLLEGNAHYRCDFRTTYKAKEKGVKLPGAHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDNARR Source: (gene. exp.) ![]() ![]() Gene: UBI4, SCD2, YLL039C / Production host: ![]() ![]() |
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-Non-polymers , 3 types, 14 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ADP.gif)
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#5: Chemical | ChemComp-ATP / #6: Chemical | ChemComp-ADP / #7: 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 |
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Sample preparation
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