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Yorodumi- PDB-8dav: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubi... -
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-Basic information
Entry | Database: PDB / ID: 8dav | |||||||||
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Title | Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uC) | |||||||||
Components |
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Keywords | MOTOR PROTEIN / ATPASE / ATPASE COMPLEX / UBIQUITIN / SUMO / SMT3 / QUALITY CONTROL | |||||||||
Function / homology | Function and homology information 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 / 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 / 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 | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Lee, H.G. / Lima, C.D. | |||||||||
Funding support | United States, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dav.cif.gz | 771 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dav.ent.gz | 623 KB | Display | PDB format |
PDBx/mmJSON format | 8dav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dav_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8dav_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8dav_validation.xml.gz | 131.1 KB | Display | |
Data in CIF | 8dav_validation.cif.gz | 192.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/8dav ftp://data.pdbj.org/pub/pdb/validation_reports/da/8dav | HTTPS FTP |
-Related structure data
Related structure data | 27277MC 8darC 8dasC 8datC 8dauC 8dawC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Saccharomyces cerevisiae (brewer's yeast) Gene: CDC48, YDL126C / Production host: Escherichia coli (E. coli) / References: UniProt: P25694, vesicle-fusing ATPase #2: Protein | | Mass: 66144.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NPL4, HRD4, YBR170C, YBR1231 / Production host: Escherichia coli (E. coli) / References: UniProt: P33755 #3: Protein | | Mass: 40001.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UFD1, PIP3, YGR048W / Production host: Escherichia coli (E. coli) / References: UniProt: P53044 #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 ubiquitin with a K48-linked polyubiquitin. Sequence of the unmodified substrate ...Details: ubiquitin that is part of the SUMO-ubiquitin(K48polyUb)-mEOS substrate; SUMO-ubiquitin-mEOS modified on K48 of ubiquitin with a K48-linked polyubiquitin. Sequence of the unmodified substrate is MGSSHHHHHHSSGENLYFQGHMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSHMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMSAIKPDMKIKLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAKYPDNIQDYFKQSFPKGYSWERSLTFEDGGICNARNDITMEGDTFYNKVRFYGTNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDIEMALLLEGNAHYRCDFRTTYKAKEKGVKLPGAHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDNARR Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UBI4, SCD2, YLL039C / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG63 |
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-Non-polymers , 3 types, 14 molecules
#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 |
-Sample preparation
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