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- EMDB-24935: CryoEM map of yeast Ubr1 in complex with monoubiquitinated N-degron -

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Basic information

Entry
Database: EMDB / ID: EMD-24935
TitleCryoEM map of yeast Ubr1 in complex with monoubiquitinated N-degron
Map data
Sampleyeast 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 speciesSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.04 Å
AuthorsPan M / Zheng Q / Zhao M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionSep 20, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateNov 24, 2021-
Current statusNov 24, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_24935.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 272.64 Å
1.07 Å/pix.
x 256 pix.
= 272.64 Å
1.07 Å/pix.
x 256 pix.
= 272.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.010419356 - 0.038645662
Average (Standard dev.)-3.3305446e-06 (±0.0014576091)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z272.640272.640272.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0100.039-0.000

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Supplemental data

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Half map: #2

Fileemd_24935_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_24935_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire yeast Ubr1 in complex with a monoubiquitinated N-degron peptide

EntireName: yeast Ubr1 in complex with a monoubiquitinated N-degron peptide
Number of Components: 1

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Component #1: protein, yeast Ubr1 in complex with a monoubiquitinated N-degron ...

ProteinName: yeast Ubr1 in complex with a monoubiquitinated N-degron peptide
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 48 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 81000.0 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 193669
3D reconstructionResolution: 6.04 Å / Resolution Method: FSC 0.143 CUT-OFF

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