+Open data
-Basic information
Entry | Database: PDB / ID: 8j1r | ||||||
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Title | cryo-EM structures of Ufd4 in complex with Ubc4-Ub | ||||||
Components |
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Keywords | LIGASE / Ufd4 / Ubc4 / Ubc4-Ub / HECT-type E3 ligase | ||||||
Function / homology | Function and homology information proteasome regulatory particle binding / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / mitochondria-associated ubiquitin-dependent protein catabolic process / cytoplasm protein quality control by the ubiquitin-proteasome system / free ubiquitin chain polymerization / protein K29-linked ubiquitination / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase ...proteasome regulatory particle binding / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / mitochondria-associated ubiquitin-dependent protein catabolic process / cytoplasm protein quality control by the ubiquitin-proteasome system / free ubiquitin chain polymerization / protein K29-linked ubiquitination / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase / Transferases; Acyltransferases; Aminoacyltransferases / ribosome-associated ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase complex / rescue of stalled ribosome / ubiquitin binding / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein-macromolecule adaptor activity / cellular response to heat / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / mitochondrion / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å | ||||||
Authors | Ai, H.S. / Mao, J.X. / Wu, X.W. / Cai, H.Y. / Pan, M. / Liu, L. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structural Visualization of HECT-E3 Ufd4 accepting and transferring Ubiquitin to Form K29/K48-branched Polyubiquitination on N-degron. bioRxiv,doi: ttps://doi.org/10.1101/2023.05.23.542033 Authors: Mao, J.X. / Ai, H.S. / Wu, X.W. / Cai, H.Y. / Pan, M. / Liu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j1r.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j1r.ent.gz | 123.7 KB | Display | PDB format |
PDBx/mmJSON format | 8j1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j1r_validation.pdf.gz | 995.3 KB | Display | wwPDB validaton report |
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Full document | 8j1r_full_validation.pdf.gz | 1010.7 KB | Display | |
Data in XML | 8j1r_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 8j1r_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/8j1r ftp://data.pdbj.org/pub/pdb/validation_reports/j1/8j1r | HTTPS FTP |
-Related structure data
Related structure data | 35931MC 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
#1: Protein | Mass: 168026.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UFD4, YKL010C, YKL162 / Production host: Saccharomyces cerevisiae BY4741 (yeast) References: UniProt: P33202, Transferases; Acyltransferases; Aminoacyltransferases, HECT-type E3 ubiquitin transferase |
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#2: Protein | Mass: 16442.586 Da / Num. of mol.: 1 / Mutation: C22S,C108S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UBC4, YBR082C, YBR0745 / Production host: Escherichia coli (E. coli) References: UniProt: P15731, E2 ubiquitin-conjugating enzyme |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||||||
Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 43.347 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124116 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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