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- EMDB-16902: 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native) -
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Open data
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Basic information
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Title | 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native) | ||||||||||||||||||
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![]() | RIBOSOME / 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 / endoplasmic reticulum Sec complex / pronephric nephron development / endoplasmic reticulum quality control compartment / regulation of proteasomal ubiquitin-dependent protein catabolic process / cotranslational protein targeting to membrane / Ssh1 translocon complex / lamin filament / positive regulation of I-kappaB phosphorylation / Sec61 translocon complex / regulation of fatty acid biosynthetic process / positive regulation of cell cycle G1/S phase transition / protein targeting to ER / protein localization to endoplasmic reticulum / regulation of megakaryocyte differentiation / protein insertion into ER membrane / 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 / signal sequence binding / TORC2 complex binding / mitotic G2/M transition checkpoint / post-translational protein targeting to membrane, translocation / Transferases; Acyltransferases; Aminoacyltransferases / GAIT complex / SRP-dependent cotranslational protein targeting to membrane, translocation / 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 / epidermal growth factor binding / optic nerve development / negative regulation of ubiquitin protein ligase activity / response to L-glutamate / regulation of neuron differentiation / retrograde protein transport, ER to cytosol / response to aldosterone / retinal ganglion cell axon guidance / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||
![]() | Penchev I / DaRosa PA / 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 484.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 80.9 KB 80.9 KB | Display Display | ![]() |
Images | ![]() | 65.3 KB | ||
Filedesc metadata | ![]() | 16.5 KB | ||
Others | ![]() ![]() | 486.9 MB 486.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8oj0MC ![]() 8ohdC ![]() 8oj5C ![]() 8oj8C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.727 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_16902_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16902_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : 60S ribosomal subunit bound to the E3-UFM1 complex and Sec61
+Supramolecule #1: 60S ribosomal subunit bound to the E3-UFM1 complex and Sec61
+Supramolecule #2: 60S ribosomal subunit
+Supramolecule #3: E3 UFM1-protein ligase 1
+Macromolecule #1: Protein transport protein Sec61 subunit alpha isoform 1
+Macromolecule #2: Protein transport protein Sec61 subunit gamma
+Macromolecule #3: Protein transport protein Sec61 subunit beta
+Macromolecule #7: E3 UFM1-protein ligase 1
+Macromolecule #8: CDK5 regulatory subunit-associated protein 3
+Macromolecule #9: DDRGK domain-containing protein 1
+Macromolecule #10: Ubiquitin-fold modifier 1
+Macromolecule #11: Eukaryotic translation initiation factor 6
+Macromolecule #12: 60S ribosomal protein L8
+Macromolecule #13: 60S ribosomal protein L3
+Macromolecule #14: 60S ribosomal protein L4
+Macromolecule #15: 60S ribosomal protein L5
+Macromolecule #16: 60S ribosomal protein L6
+Macromolecule #17: 60S ribosomal protein L7
+Macromolecule #18: 60S ribosomal protein L7a
+Macromolecule #19: 60S ribosomal protein L9
+Macromolecule #20: Ribosomal protein uL16-like
+Macromolecule #21: 60S ribosomal protein L11
+Macromolecule #22: 60S ribosomal protein L13
+Macromolecule #23: 60S ribosomal protein L14
+Macromolecule #24: 60S ribosomal protein L15
+Macromolecule #25: 60S ribosomal protein L13a
+Macromolecule #26: 60S ribosomal protein L17
+Macromolecule #27: 60S ribosomal protein L18
+Macromolecule #28: 60S ribosomal protein L19
+Macromolecule #29: 60S ribosomal protein L18a
+Macromolecule #30: 60S ribosomal protein L21
+Macromolecule #31: 60S ribosomal protein L22
+Macromolecule #32: 60S ribosomal protein L23
+Macromolecule #33: 60S ribosomal protein L24
+Macromolecule #34: 60S ribosomal protein L23a
+Macromolecule #35: 60S ribosomal protein L26
+Macromolecule #36: 60S ribosomal protein L27
+Macromolecule #37: 60S ribosomal protein L27a
+Macromolecule #38: 60S ribosomal protein L29
+Macromolecule #39: 60S ribosomal protein L30
+Macromolecule #40: 60S ribosomal protein L31
+Macromolecule #41: 60S ribosomal protein L32
+Macromolecule #42: 60S ribosomal protein L35a
+Macromolecule #43: 60S ribosomal protein L34
+Macromolecule #44: 60S ribosomal protein L35
+Macromolecule #45: 60S ribosomal protein L36
+Macromolecule #46: 60S ribosomal protein L37
+Macromolecule #47: 60S ribosomal protein L38
+Macromolecule #48: 60S ribosomal protein L39
+Macromolecule #49: Ubiquitin-60S ribosomal protein L40
+Macromolecule #50: 60S ribosomal protein L36a
+Macromolecule #51: 60S ribosomal protein L37a
+Macromolecule #52: 60S ribosomal protein L28
+Macromolecule #53: 60S ribosomal protein L10a
+Macromolecule #4: 28S rRNA
+Macromolecule #5: 5S rRNA
+Macromolecule #6: 5.8S rRNA
+Macromolecule #54: MAGNESIUM ION
+Macromolecule #55: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20377 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |