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- PDB-8ohd: 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native) -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ohd | ||||||||||||||||||
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Title | 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native) | ||||||||||||||||||
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![]() | RIBOSOME / 60S / UFMylation / ER / recycling | ||||||||||||||||||
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 / lamin filament / positive regulation of I-kappaB phosphorylation / regulation of fatty acid biosynthetic process / positive regulation of cell cycle G1/S phase transition / protein localization to endoplasmic reticulum / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / eukaryotic 80S initiation complex / miRNA-mediated gene silencing by inhibition of translation / negative regulation of protein neddylation / translation at presynapse / regulation of intracellular estrogen receptor signaling pathway / axial mesoderm development / positive regulation of proteasomal protein catabolic process / negative regulation of formation of translation preinitiation complex / negative regulation of protein serine/threonine kinase activity / ribosomal protein import into nucleus / 90S preribosome assembly / TORC2 complex binding / mitotic G2/M transition checkpoint / Transferases; Acyltransferases; Aminoacyltransferases / GAIT complex / middle ear morphogenesis / cartilage development / regulation of canonical NF-kappaB signal transduction / reticulophagy / cytoplasmic side of rough endoplasmic reticulum membrane / mitogen-activated protein kinase binding / A band / regulation of reactive oxygen species metabolic process / regulation of G1 to G0 transition / exit from mitosis / alpha-beta T cell differentiation / regulation of glycolytic process / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / negative regulation of ubiquitin protein ligase activity / response to L-glutamate / regulation of neuron differentiation / response to aldosterone / retinal ganglion cell axon guidance / negative regulation of protein import into nucleus / G1 to G0 transition / regulation of cyclin-dependent protein serine/threonine kinase activity / homeostatic process / lung morphogenesis / negative regulation of NF-kappaB transcription factor activity / maturation of 5.8S rRNA / Protein hydroxylation / male meiosis I / ubiquitin-like protein ligase binding / macrophage chemotaxis / Peptide chain elongation / mitotic G2 DNA damage checkpoint signaling / ribosomal large subunit binding / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / preribosome, large subunit precursor / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / protein localization to nucleus / 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 / protein-RNA complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein targeting / cellular response to interleukin-4 / endomembrane system / cellular response to actinomycin D / positive regulation of autophagy / cytosolic ribosome / ribosomal subunit export from nucleus / rough endoplasmic reticulum Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
![]() | Penchev, I. / DaRosa, P.A. / Becker, T. / Beckmann, R. / Kopito, R. | ||||||||||||||||||
Funding support | European Union, ![]() ![]() ![]()
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![]() | ![]() Title: UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. Authors: Paul A DaRosa / Ivan Penchev / Samantha C Gumbin / Francesco Scavone / Magda Wąchalska / Joao A Paulo / Alban Ordureau / Joshua J Peter / Yogesh Kulathu / J Wade Harper / Thomas Becker / ...Authors: Paul A DaRosa / Ivan Penchev / Samantha C Gumbin / Francesco Scavone / Magda Wąchalska / Joao A Paulo / Alban Ordureau / Joshua J Peter / Yogesh Kulathu / J Wade Harper / Thomas Becker / Roland Beckmann / Ron R Kopito / ![]() ![]() ![]() Abstract: Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour. UFM1 is a UBL that ...Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour. UFM1 is a UBL that predominantly modifies a single lysine residue on a single ribosomal protein, uL24 (also called RPL26), on ribosomes at the cytoplasmic surface of the endoplasmic reticulum (ER). UFM1 conjugation (UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER. Neither the molecular mechanism by which the UFMylation machinery achieves such precise target selection nor how this ribosomal modification promotes 60S rescue is known. Here we show that ribosome UFMylation in vivo occurs on free 60S and we present sequential cryo-electron microscopy snapshots of the heterotrimeric UFM1 E3 ligase (E3(UFM1)) engaging its substrate uL24. E3(UFM1) binds the L1 stalk, empty transfer RNA-binding sites and the peptidyl transferase centre through carboxy-terminal domains of UFL1, which results in uL24 modification more than 150 Å away. After catalysing UFM1 transfer, E3(UFM1) remains stably bound to its product, UFMylated 60S, forming a C-shaped clamp that extends all the way around the 60S from the transfer RNA-binding sites to the polypeptide tunnel exit. Our structural and biochemical analyses suggest a role for E3(UFM1) in post-termination release and recycling of the large ribosomal subunit from the ER membrane. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 3.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 221.8 KB | Display | |
Data in CIF | ![]() | 396.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 16880MC ![]() 8oj0C ![]() 8oj5C ![]() 8oj8C 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
-RNA chain , 3 types, 3 molecules 578
#1: RNA chain | Mass: 1640166.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: RNA chain | Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: RNA chain | Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 7 types, 7 molecules ABCDKLILm
#4: Protein | Mass: 89722.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: O94874, Transferases; Acyltransferases; Aminoacyltransferases |
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#5: Protein | Mass: 56977.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 35663.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 9128.552 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 26620.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#17: Protein | Mass: 24552.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#46: Protein | Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+60S ribosomal protein ... , 40 types, 40 molecules LALBLCLDLELFLGLHLJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLeLf...
-Non-polymers , 2 types, 225 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#51: Chemical | ChemComp-MG / #52: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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-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 |
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Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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 defocus max: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123096 / Symmetry type: POINT |