+Open data
-Basic information
Entry | Database: PDB / ID: 7mex | ||||||
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Title | Structure of yeast Ubr1 in complex with Ubc2 and N-degron | ||||||
Components |
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Keywords | TRANSFERASE / Ubiquitin E3 ligase / ubiquitination / Ubr1 / Ubc2 / Degron / N-end rule | ||||||
Function / homology | Function and homology information MUB1-RAD6-UBR2 ubiquitin ligase complex / RAD6-UBR2 ubiquitin ligase complex / sno(s)RNA transcription / Rad6-Rad18 complex / regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / HULC complex / error-free postreplication DNA repair / proteasome regulatory particle binding / stress-induced homeostatically regulated protein degradation pathway ...MUB1-RAD6-UBR2 ubiquitin ligase complex / RAD6-UBR2 ubiquitin ligase complex / sno(s)RNA transcription / Rad6-Rad18 complex / regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / HULC complex / error-free postreplication DNA repair / proteasome regulatory particle binding / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / meiotic DNA double-strand break formation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / telomere maintenance via recombination / proteasome regulatory particle, base subcomplex / ribosome-associated ubiquitin-dependent protein catabolic process / DNA duplex unwinding / E2 ubiquitin-conjugating enzyme / error-free translesion synthesis / sporulation resulting in formation of a cellular spore / proteasome binding / protein monoubiquitination / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / subtelomeric heterochromatin formation / cellular response to unfolded protein / error-prone translesion synthesis / ERAD pathway / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / mitotic G1 DNA damage checkpoint signaling / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å | ||||||
Authors | Pan, M. / Zheng, Q. / Wang, T. / Liang, L. / Yu, Y. / Liu, L. / Zhao, M. | ||||||
Funding support | 1items
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Citation | Journal: Nature / Year: 2021 Title: Structural insights into Ubr1-mediated N-degron polyubiquitination. Authors: Man Pan / Qingyun Zheng / Tian Wang / Lujun Liang / Junxiong Mao / Chong Zuo / Ruichao Ding / Huasong Ai / Yuan Xie / Dong Si / Yuanyuan Yu / Lei Liu / Minglei Zhao / Abstract: The N-degron pathway targets proteins that bear a destabilizing residue at the N terminus for proteasome-dependent degradation. In yeast, Ubr1-a single-subunit E3 ligase-is responsible for the Arg/N- ...The N-degron pathway targets proteins that bear a destabilizing residue at the N terminus for proteasome-dependent degradation. In yeast, Ubr1-a single-subunit E3 ligase-is responsible for the Arg/N-degron pathway. How Ubr1 mediates the initiation of ubiquitination and the elongation of the ubiquitin chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown. Here we developed chemical strategies to mimic the reaction intermediates of the first and second ubiquitin transfer steps, and determined the cryo-electron microscopy structures of Ubr1 in complex with Ubc2, ubiquitin and two N-degron peptides, representing the initiation and elongation steps of ubiquitination. Key structural elements, including a Ubc2-binding region and an acceptor ubiquitin-binding loop on Ubr1, were identified and characterized. These structures provide mechanistic insights into the initiation and elongation of ubiquitination catalysed by Ubr1. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7mex.cif.gz | 365.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mex.ent.gz | 288.5 KB | Display | PDB format |
PDBx/mmJSON format | 7mex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/7mex ftp://data.pdbj.org/pub/pdb/validation_reports/me/7mex | HTTPS FTP |
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-Related structure data
Related structure data | 23806MC 7meyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10886 (Title: Single-particle cryoEM data of yeast Ubr1-Ubc2-Ub-N-degron complex (initiation) Data size: 5.7 TB Data #1: Unaligned movie data of yeast Ubr1-Ubc2-Ub-N-degron complex (initiation complex) [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 8622.922 Da / Num. of mol.: 1 / Mutation: G76C / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG48 | ||
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#2: Protein | Mass: 17203.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RAD6, UBC2, YGL058W / Plasmid: p416CYC / Production host: Saccharomyces cerevisiae S288C (yeast) References: UniProt: P06104, E2 ubiquitin-conjugating enzyme | ||
#3: Protein/peptide | Mass: 4571.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288C (yeast) | ||
#4: Protein | Mass: 225102.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: UBR1, PTR1, YGR184C, G7168 / Plasmid: p416CYC / Production host: Saccharomyces cerevisiae S288C (yeast) References: UniProt: P19812, RING-type E3 ubiquitin transferase | ||
#5: Chemical | ChemComp-ZN / Has ligand of interest | N | |
-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 | Name: yeast Ubr1 in complex with Ubc2 and N-degron / Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Buffer solution | pH: 8 |
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 / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232915 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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