+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11456 | ||||||||||||
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Title | EDF1-ribosome complex | ||||||||||||
Map data | Map of EDF1 bound to 80S ribosomes, (local resolution filtered). | ||||||||||||
Sample |
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Function / homology | Function and homology information endothelial cell differentiation / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation ...endothelial cell differentiation / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / nucleolus organization / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / laminin receptor activity / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / NF-kappaB complex / transcription regulator inhibitor activity / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / pigmentation / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / erythrocyte development / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / positive regulation of transcription by RNA polymerase I / positive regulation of activated T cell proliferation / fibroblast growth factor binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / iron-sulfur cluster binding / TOR signaling / BH3 domain binding / mTORC1-mediated signalling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / Selenocysteine synthesis / monocyte chemotaxis / cysteine-type endopeptidase activator activity involved in apoptotic process / Formation of a pool of free 40S subunits / ribosomal small subunit export from nucleus / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / TFIID-class transcription factor complex binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / regulation of lipid metabolic process / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of respiratory burst involved in inflammatory response / photoreceptor outer segment / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / gastrulation / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rough endoplasmic reticulum / spindle assembly / regulation of translational fidelity / MDM2/MDM4 family protein binding / positive regulation of DNA binding / laminin binding / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / negative regulation of smoothened signaling pathway / rescue of stalled ribosome / signaling adaptor activity / positive regulation of cell cycle / negative regulation of peptidyl-serine phosphorylation / positive regulation of phagocytosis / stress granule assembly / translation initiation factor binding / maturation of SSU-rRNA Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Human (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||
Authors | Best KM / Denk T / Cheng J / Thoms M / Berninghausen O / Beckmann R | ||||||||||||
Funding support | Germany, United States, 3 items
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Citation | Journal: Elife / Year: 2020 Title: EDF1 coordinates cellular responses to ribosome collisions. Authors: Niladri K Sinha / Alban Ordureau / Katharina Best / James A Saba / Boris Zinshteyn / Elayanambi Sundaramoorthy / Amit Fulzele / Danielle M Garshott / Timo Denk / Matthias Thoms / Joao A ...Authors: Niladri K Sinha / Alban Ordureau / Katharina Best / James A Saba / Boris Zinshteyn / Elayanambi Sundaramoorthy / Amit Fulzele / Danielle M Garshott / Timo Denk / Matthias Thoms / Joao A Paulo / J Wade Harper / Eric J Bennett / Roland Beckmann / Rachel Green / Abstract: Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation ...Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation combined with quantitative proteomics to systematically identify proteins associated with collided ribosomes. This approach identified Endothelial differentiation-related factor 1 (EDF1) as a novel protein recruited to collided ribosomes during translational distress. Cryo-electron microscopic analyses of EDF1 and its yeast homolog Mbf1 revealed a conserved 40S ribosomal subunit binding site at the mRNA entry channel near the collision interface. EDF1 recruits the translational repressors GIGYF2 and EIF4E2 to collided ribosomes to initiate a negative-feedback loop that prevents new ribosomes from translating defective mRNAs. Further, EDF1 regulates an immediate-early transcriptional response to ribosomal collisions. Our results uncover mechanisms through which EDF1 coordinates multiple responses of the ribosome-mediated quality control pathway and provide novel insights into the intersection of ribosome-mediated quality control with global transcriptional regulation. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11456.map.gz | 139.6 MB | EMDB map data format | |
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Header (meta data) | emd-11456-v30.xml emd-11456.xml | 49.8 KB 49.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11456_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_11456.png | 208.4 KB | ||
Masks | emd_11456_msk_1.map | 244.1 MB | Mask map | |
Others | emd_11456_additional.map.gz emd_11456_half_map_1.map.gz emd_11456_half_map_2.map.gz | 17.8 MB 192.9 MB 192.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11456 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11456 | HTTPS FTP |
-Related structure data
Related structure data | 6zvhMC 6zviC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11456.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of EDF1 bound to 80S ribosomes, (local resolution filtered). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11456_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Post processed map, bFactor -30
File | emd_11456_additional.map | ||||||||||||
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Annotation | Post processed map, bFactor -30 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of the 3D refinement
File | emd_11456_half_map_1.map | ||||||||||||
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Annotation | Half map 2 of the 3D refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of the 3D refinement
File | emd_11456_half_map_2.map | ||||||||||||
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Annotation | Half map 1 of the 3D refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : EDF1-ribosome complex
+Supramolecule #1: EDF1-ribosome complex
+Macromolecule #1: 18S rRNA
+Macromolecule #35: E-site tRNA
+Macromolecule #2: 40S ribosomal protein SA
+Macromolecule #3: 40S ribosomal protein S3a
+Macromolecule #4: 40S ribosomal protein S3
+Macromolecule #5: 40S ribosomal protein S4, X isoform
+Macromolecule #6: 40S ribosomal protein S5
+Macromolecule #7: 40S ribosomal protein S7
+Macromolecule #8: 40S ribosomal protein S8
+Macromolecule #9: 40S ribosomal protein S10
+Macromolecule #10: 40S ribosomal protein S11
+Macromolecule #11: 40S ribosomal protein S15
+Macromolecule #12: 40S ribosomal protein S16
+Macromolecule #13: 40S ribosomal protein S17
+Macromolecule #14: 40S ribosomal protein S18
+Macromolecule #15: 40S ribosomal protein S19
+Macromolecule #16: 40S ribosomal protein S20
+Macromolecule #17: 40S ribosomal protein S21
+Macromolecule #18: 40S ribosomal protein S23
+Macromolecule #19: 40S ribosomal protein S26
+Macromolecule #20: 40S ribosomal protein S28
+Macromolecule #21: 40S ribosomal protein S29
+Macromolecule #22: Receptor of activated protein C kinase 1
+Macromolecule #23: 40S ribosomal protein S2
+Macromolecule #24: 40S ribosomal protein S6
+Macromolecule #25: 40S ribosomal protein S9
+Macromolecule #26: 40S ribosomal protein S12
+Macromolecule #27: 40S ribosomal protein S13
+Macromolecule #28: 40S ribosomal protein S14
+Macromolecule #29: 40S ribosomal protein S15a
+Macromolecule #30: 40S ribosomal protein S24
+Macromolecule #31: 40S ribosomal protein S25
+Macromolecule #32: 40S ribosomal protein S27
+Macromolecule #33: 40S ribosomal protein S30
+Macromolecule #34: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #36: Cell growth-regulating nucleolar protein
+Macromolecule #37: Endothelial differentiation-related factor 1
+Macromolecule #38: MAGNESIUM ION
+Macromolecule #39: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 28.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |