|Entry||Database: EMDB / ID: EMD-24935|
|Title||CryoEM map of yeast Ubr1 in complex with monoubiquitinated N-degron|
|Sample||yeast Ubr1 in complex with a monoubiquitinated N-degron peptide|
|Function / homology|
Function and homology information
MUB1-RAD6-UBR2 ubiquitin ligase complex / Rad6-Rad18 complex / regulation of dipeptide transport / HULC complex / UBR1-RAD6 ubiquitin ligase complex / stress-induced homeostatically regulated protein degradation pathway / error-free postreplication DNA repair / ubiquitin-dependent protein catabolic process via the N-end rule pathway / proteasome regulatory particle binding / ribosome-associated ubiquitin-dependent protein catabolic process ...MUB1-RAD6-UBR2 ubiquitin ligase complex / Rad6-Rad18 complex / regulation of dipeptide transport / HULC complex / UBR1-RAD6 ubiquitin ligase complex / stress-induced homeostatically regulated protein degradation pathway / error-free postreplication DNA repair / ubiquitin-dependent protein catabolic process via the N-end rule pathway / proteasome regulatory particle binding / ribosome-associated ubiquitin-dependent protein catabolic process / cytoplasm protein quality control by the ubiquitin-proteasome system / meiotic DNA double-strand break formation / mitochondria-associated ubiquitin-dependent protein catabolic process / telomere maintenance via recombination / histone ubiquitination / histone monoubiquitination / DNA duplex unwinding / proteasome regulatory particle, base subcomplex / Antigen processing: Ubiquitination & Proteasome degradation / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / proteasome binding / protein K63-linked ubiquitination / subtelomeric heterochromatin assembly => GO:0031509 / ubiquitin conjugating enzyme activity / sporulation resulting in formation of a cellular spore / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / Myoclonic epilepsy of Lafora / ER Quality Control Compartment (ERQC) / endoplasmic reticulum mannose trimming / ubiquitin-dependent ERAD pathway / Glycogen synthesis / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / mitotic G1 DNA damage checkpoint signaling / TICAM1,TRAF6-dependent induction of TAK1 complex / Constitutive Signaling by NOTCH1 HD Domain Mutants / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Endosomal Sorting Complex Required For Transport (ESCRT) / TICAM1-dependent activation of IRF3/IRF7 / endoplasmic reticulum quality control compartment / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / MyD88-independent toll-like receptor signaling pathway / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / DDX58/IFIH1-mediated induction of interferon-alpha/beta / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of ERBB2:ERBB3 signaling / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / nucleotide-binding oligomerization domain containing signaling pathway / NF-kB is activated and signals survival / Regulation of PTEN localization / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon / Josephin domain DUBs / regulation of exit from mitosis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Gap-filling DNA repair synthesis and ligation in GG-NER / TRIF-dependent toll-like receptor signaling pathway / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / Downregulation of TGF-beta receptor signaling / IKK complex recruitment mediated by RIP1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / nucleotide-excision repair, DNA damage recognition / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / CDT1 association with the CDC6:ORC:origin complex / nucleotide-excision repair, DNA gap filling / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Autodegradation of Cdh1 by Cdh1:APC/C / global genome nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / Asymmetric localization of PCP proteins / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Degradation of DVL
Similarity search - Function
Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR-like, C-terminal / E3 ubiquitin-protein ligase UBR1-like / Putative zinc finger in N-recognin (UBR box) / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Zinc finger UBR-type profile. / Zinc finger, UBR-type / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating (UBC) core domain profile. ...Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR-like, C-terminal / E3 ubiquitin-protein ligase UBR1-like / Putative zinc finger in N-recognin (UBR box) / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Zinc finger UBR-type profile. / Zinc finger, UBR-type / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 2 / Polyubiquitin-C / E3 ubiquitin-protein ligase UBR1
Similarity search - Component
|Biological species||Saccharomyces cerevisiae (baker's yeast)|
|Method||single particle reconstruction / cryo EM / Resolution: 6.04 Å|
|Authors||Pan M / Zheng Q / Zhao M|
|Funding support||1 items |
|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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_24935.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.065 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Half map: #2
|Projections & Slices|
-Half map: #1
-Entire yeast Ubr1 in complex with a monoubiquitinated N-degron peptide
|Entire||Name: yeast Ubr1 in complex with a monoubiquitinated N-degron peptide|
Number of Components: 1
-Component #1: protein, yeast Ubr1 in complex with a monoubiquitinated N-degron ...
|Protein||Name: yeast Ubr1 in complex with a monoubiquitinated N-degron peptide|
Recombinant expression: No
|Source||Species: Saccharomyces cerevisiae (baker's yeast)|
|Source (engineered)||Expression System: Saccharomyces cerevisiae (baker's yeast)|
|Specimen||Specimen State: Particle / Method: cryo EM|
|Sample solution||pH: 8|
|Vitrification||Cryogen Name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 48 e/Å2 / Illumination Mode: FLOOD BEAM|
|Lens||Magnification: 81000.0 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Processing||Method: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 193669|
|3D reconstruction||Resolution: 6.04 Å / Resolution Method: FSC 0.143 CUT-OFF|
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