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Open data
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Basic information
Entry | Database: PDB / ID: 8qfc | |||||||||||||||
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Title | UFL1 E3 ligase bound 60S ribosome | |||||||||||||||
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![]() | LIGASE / UFM1 / Ribosome / Complex | |||||||||||||||
Function / homology | ![]() UFM1 ligase activity / regulation of phosphatase activity / apoptotic nuclear changes / definitive erythrocyte differentiation / positive regulation of metallopeptidase activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to endoplasmic reticulum ...UFM1 ligase activity / regulation of phosphatase activity / apoptotic nuclear changes / definitive erythrocyte differentiation / positive regulation of metallopeptidase activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to endoplasmic reticulum / negative regulation of protein kinase activity by regulation of protein phosphorylation / negative regulation of IRE1-mediated unfolded protein response / regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of I-kappaB phosphorylation / positive regulation of cell cycle G1/S phase transition / protein localization to endoplasmic reticulum / regulation of intracellular estrogen receptor signaling pathway / positive regulation of proteasomal protein catabolic process / negative regulation of protein serine/threonine kinase activity / mitotic G2/M transition checkpoint / Transferases; Acyltransferases; Aminoacyltransferases / cartilage development / regulation of canonical NF-kappaB signal transduction / reticulophagy / mitogen-activated protein kinase binding / response to L-glutamate / regulation of neuron differentiation / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of NF-kappaB transcription factor activity / ubiquitin-like protein ligase binding / Peptide chain elongation / mitotic G2 DNA damage checkpoint signaling / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / NF-kappaB binding / RHOA GTPase cycle / hematopoietic stem cell differentiation / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / endomembrane system / positive regulation of autophagy / cytosolic ribosome / endoplasmic reticulum unfolded protein response / positive regulation of glial cell proliferation / MDM2/MDM4 family protein binding / negative regulation of protein ubiquitination / regulation of mitotic cell cycle / response to endoplasmic reticulum stress / cyclin binding / erythrocyte differentiation / negative regulation of protein phosphorylation / maturation of LSU-rRNA / liver development / negative regulation of MAP kinase activity / DNA damage checkpoint signaling / positive regulation of protein ubiquitination / regulation of protein stability / negative regulation of protein catabolic process / brain development / Regulation of expression of SLITs and ROBOs / positive regulation of protein localization to nucleus / osteoblast differentiation / regulation of protein localization / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of NF-kappaB transcription factor activity / site of double-strand break / regulation of inflammatory response / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / cell population proliferation / cytosolic large ribosomal subunit / cytoplasmic translation / postsynaptic density / positive regulation of cell migration / structural constituent of ribosome / neuron projection / translation / negative regulation of gene expression / intracellular membrane-bounded organelle / DNA repair / focal adhesion / centrosome / DNA damage response / positive regulation of cell population proliferation / positive regulation of gene expression / endoplasmic reticulum membrane / nucleolus / negative regulation of apoptotic process / protein kinase binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
![]() | Makhlouf, L. / Zeqiraj, E. / Kulathu, Y. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons. Authors: Linda Makhlouf / Joshua J Peter / Helge M Magnussen / Rohan Thakur / David Millrine / Thomas C Minshull / Grace Harrison / Joby Varghese / Frederic Lamoliatte / Martina Foglizzo / Thomas ...Authors: Linda Makhlouf / Joshua J Peter / Helge M Magnussen / Rohan Thakur / David Millrine / Thomas C Minshull / Grace Harrison / Joby Varghese / Frederic Lamoliatte / Martina Foglizzo / Thomas Macartney / Antonio N Calabrese / Elton Zeqiraj / Yogesh Kulathu / ![]() Abstract: Stalled ribosomes at the endoplasmic reticulum (ER) are covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit protein RPL26 (also known as uL24). This modification, ...Stalled ribosomes at the endoplasmic reticulum (ER) are covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit protein RPL26 (also known as uL24). This modification, which is known as UFMylation, is orchestrated by the UFM1 ribosome E3 ligase (UREL) complex, comprising UFL1, UFBP1 and CDK5RAP3 (ref. ). However, the catalytic mechanism of UREL and the functional consequences of UFMylation are unclear. Here we present cryo-electron microscopy structures of UREL bound to 60S ribosomes, revealing the basis of its substrate specificity. UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other. A UFL1 loop inserts into and remodels the peptidyl transferase centre. These features of UREL suggest a crucial function for UFMylation in the release and recycling of stalled or terminated ribosomes from the ER membrane. In the absence of functional UREL, 60S-SEC61 translocon complexes accumulate at the ER membrane, demonstrating that UFMylation is necessary for releasing SEC61 from 60S subunits. Notably, this release is facilitated by a functional switch of UREL from a 'writer' to a 'reader' module that recognizes its product-UFMylated 60S ribosomes. Collectively, we identify a fundamental role for UREL in dissociating 60S subunits from the SEC61 translocon and the basis for UFMylation in regulating protein homeostasis at the ER. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.7 KB | Display | ![]() |
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PDB format | ![]() | 227.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 764.9 KB | Display | ![]() |
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Full document | ![]() | 776.1 KB | Display | |
Data in XML | ![]() | 61.1 KB | Display | |
Data in CIF | ![]() | 90.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18381MC ![]() 8bzrC ![]() 8c0dC ![]() 8qfdC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 24879.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 91591.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O94874, Transferases; Acyltransferases; Aminoacyltransferases |
#3: Protein | Mass: 57458.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 34644.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 9236.628 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: UFM1 ribosome E3 ligase complex bound to 60S ribosome / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 Details: 25 mM HEPES pH 7.5, 50 mM KCl, 5 mM MgCl2, 2 mM DTT |
Specimen | Conc.: 7.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 200 nm |
Image recording | Average exposure time: 2.67 sec. / Electron dose: 33.4 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 59394 |
EM imaging optics | Energyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 299008 / Symmetry type: POINT | ||||||||||||||||||||||||
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