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Yorodumi- EMDB-44464: 80S ribosome bound with angiogenin and complex of eEF1A and Ala-t... -
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Open data
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Basic information
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| Title | 80S ribosome bound with angiogenin and complex of eEF1A and Ala-tRNAAla | |||||||||
Map data | 80S ribosome bound with angiogenin and complex of eEF1A and Ala-tRNAAla, main map used for model refinement | |||||||||
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Keywords | Angiogenin / RNase / RIBOSOME | |||||||||
| Function / homology | Function and homology informationEukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / angiogenin-PRI complex / negative regulation of translation in response to stress / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / melatonin binding / HSF1 activation / signaling ...Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / angiogenin-PRI complex / negative regulation of translation in response to stress / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / melatonin binding / HSF1 activation / signaling / cell communication / tRNA export from nucleus / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / fungal-type vacuole membrane / Protein methylation / Adherens junctions interactions / ribosomal subunit / oocyte maturation / homeostatic process / hematopoietic stem cell proliferation / negative regulation of protein phosphorylation / rRNA transcription / actin filament bundle assembly / basement membrane / ubiquitin ligase inhibitor activity / translational elongation / positive regulation of phosphorylation / positive regulation of signal transduction by p53 class mediator / endocytic vesicle / RNA nuclease activity / 90S preribosome / translation elongation factor activity / phagocytic cup / protein-RNA complex assembly / negative regulation of protein kinase activity / ovarian follicle development / rough endoplasmic reticulum / response to hormone / ribosomal small subunit export from nucleus / translation regulator activity / gastrulation / positive regulation of endothelial cell proliferation / actin filament polymerization / MDM2/MDM4 family protein binding / Neutrophil degranulation / cytosolic ribosome / stress granule assembly / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / peptide binding / RNA endonuclease activity / cellular response to amino acid starvation / placenta development / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of protein secretion / maturation of SSU-rRNA / small-subunit processome / negative regulation of smooth muscle cell proliferation / spindle / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / actin filament binding / GDP binding / rhythmic process / antibacterial humoral response / positive regulation of canonical Wnt signaling pathway / cell migration / heparin binding / actin cytoskeleton / large ribosomal subunit / regulation of translation / chromosome / ribosome binding / actin binding / growth cone / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / angiogenesis / endonuclease activity / defense response to Gram-negative bacterium / perikaryon / killing of cells of another organism / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / cytoskeleton / tRNA binding / response to hypoxia / mitochondrial inner membrane Similarity search - Function | |||||||||
| Biological species | ![]() ![]() Homo sapiens (human) / ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Loveland AB / Korostelev AA | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2024Title: Structural mechanism of angiogenin activation by the ribosome. Authors: Anna B Loveland / Cha San Koh / Robin Ganesan / Allan Jacobson / Andrei A Korostelev / ![]() Abstract: Angiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance. After activation during cellular stress, ...Angiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance. After activation during cellular stress, angiogenin cleaves tRNAs at the anticodon loop, resulting in translation repression. However, the catalytic activity of isolated angiogenin is very low, and the mechanisms of the enzyme activation and tRNA specificity have remained a puzzle. Here we identify these mechanisms using biochemical assays and cryogenic electron microscopy (cryo-EM). Our study reveals that the cytosolic ribosome is the activator of angiogenin. A cryo-EM structure features angiogenin bound in the A site of the 80S ribosome. The C-terminal tail of angiogenin is rearranged by interactions with the ribosome to activate the RNase catalytic centre, making the enzyme several orders of magnitude more efficient in tRNA cleavage. Additional 80S-angiogenin structures capture how tRNA substrate is directed by the ribosome into angiogenin's active site, demonstrating that the ribosome acts as the specificity factor. Our findings therefore suggest that angiogenin is activated by ribosomes with a vacant A site, the abundance of which increases during cellular stress. These results may facilitate the development of therapeutics to treat cancer and neurodegenerative diseases. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_44464.map.gz | 794.3 MB | EMDB map data format | |
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| Header (meta data) | emd-44464-v30.xml emd-44464.xml | 111.9 KB 111.9 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_44464_fsc.xml | 20.6 KB | Display | FSC data file |
| Images | emd_44464.png | 191.6 KB | ||
| Filedesc metadata | emd-44464.cif.gz | 20.1 KB | ||
| Others | emd_44464_additional_1.map.gz emd_44464_half_map_1.map.gz emd_44464_half_map_2.map.gz | 794.8 MB 144.8 MB 144.8 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44464 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44464 | HTTPS FTP |
-Validation report
| Summary document | emd_44464_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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| Full document | emd_44464_full_validation.pdf.gz | 1 MB | Display | |
| Data in XML | emd_44464_validation.xml.gz | 30.1 KB | Display | |
| Data in CIF | emd_44464_validation.cif.gz | 39.9 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44464 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44464 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9bdpMC ![]() 9bdlC ![]() 9bdnC C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_44464.map.gz / Format: CCP4 / Size: 857.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | 80S ribosome bound with angiogenin and complex of eEF1A and Ala-tRNAAla, main map used for model refinement | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: 80S ribosome bound with angiogenin and complex of...
| File | emd_44464_additional_1.map | ||||||||||||
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| Annotation | 80S ribosome bound with angiogenin and complex of eEF1A and Ala-tRNAAla, map low-passed filtered to 5 A, used for placing tRNA and eEF1A | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: 80S ribosome bound with angiogenin and complex of...
| File | emd_44464_half_map_1.map | ||||||||||||
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| Annotation | 80S ribosome bound with angiogenin and complex of eEF1A and Ala-tRNAAla, half map 1 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: 80S ribosome bound with angiogenin and complex of...
| File | emd_44464_half_map_2.map | ||||||||||||
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| Annotation | 80S ribosome bound with angiogenin and complex of eEF1A and Ala-tRNAAla, half map 2 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : 80S ribosome bound with angiogenin and complex of eEF1A and Ala-t...
+Supramolecule #1: 80S ribosome bound with angiogenin and complex of eEF1A and Ala-t...
+Macromolecule #1: 18S rRNA
+Macromolecule #2: 28S rRNA
+Macromolecule #3: 5.8S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #83: tRNAfMet
+Macromolecule #84: mRNA
+Macromolecule #85: tRNAAla
+Macromolecule #5: 60S ribosomal protein L8
+Macromolecule #6: 60S ribosomal protein L3
+Macromolecule #7: 60S ribosomal protein L4
+Macromolecule #8: 60S ribosomal protein L5
+Macromolecule #9: 60S ribosomal protein L6
+Macromolecule #10: 60S ribosomal protein L7
+Macromolecule #11: Large ribosomal subunit protein eL8
+Macromolecule #12: 60S ribosomal protein L9
+Macromolecule #13: Ribosomal protein L10
+Macromolecule #14: 60S ribosomal protein L11
+Macromolecule #15: uL11
+Macromolecule #16: Large ribosomal subunit protein eL13
+Macromolecule #17: 60S ribosomal protein L14
+Macromolecule #18: 60S ribosomal protein L15
+Macromolecule #19: Large ribosomal subunit protein uL13
+Macromolecule #20: 60S ribosomal protein L17
+Macromolecule #21: Large ribosomal subunit protein eL18
+Macromolecule #22: 60S ribosomal protein L19
+Macromolecule #23: 60S ribosomal protein L18a
+Macromolecule #24: 60S ribosomal protein L21
+Macromolecule #25: Large ribosomal subunit protein eL22
+Macromolecule #26: 60S ribosomal protein L23
+Macromolecule #27: Ribosomal protein L24
+Macromolecule #28: Large ribosomal subunit protein uL23
+Macromolecule #29: 60S ribosomal protein L26
+Macromolecule #30: 60S ribosomal protein L27
+Macromolecule #31: 60S ribosomal protein L27a
+Macromolecule #32: Large ribosomal subunit protein eL29
+Macromolecule #33: 60S ribosomal protein L30
+Macromolecule #34: 60S ribosomal protein L31
+Macromolecule #35: Large ribosomal subunit protein eL32
+Macromolecule #36: 60S ribosomal protein L35a
+Macromolecule #37: 60S ribosomal protein L34
+Macromolecule #38: 60S ribosomal protein L35
+Macromolecule #39: 60S ribosomal protein L36
+Macromolecule #40: 60S ribosomal protein L37
+Macromolecule #41: Large ribosomal subunit protein eL38
+Macromolecule #42: 60S ribosomal protein L39
+Macromolecule #43: Large ribosomal subunit protein eL40
+Macromolecule #44: eL41
+Macromolecule #45: eL42
+Macromolecule #46: 60S ribosomal protein L37a
+Macromolecule #47: 60S ribosomal protein L28
+Macromolecule #48: 60S acidic ribosomal protein P0
+Macromolecule #49: Angiogenin
+Macromolecule #50: Receptor of activated protein C kinase 1
+Macromolecule #51: 40S_SA_C domain-containing protein
+Macromolecule #52: 40S ribosomal protein S3a
+Macromolecule #53: 40S ribosomal protein S2
+Macromolecule #54: 40S ribosomal protein S3
+Macromolecule #55: 40S ribosomal protein S4
+Macromolecule #56: Ribosomal protein S5
+Macromolecule #57: 40S ribosomal protein S6
+Macromolecule #58: Small ribosomal subunit protein eS7
+Macromolecule #59: 40S ribosomal protein S8
+Macromolecule #60: 40S ribosomal protein S9
+Macromolecule #61: 40S ribosomal protein S10
+Macromolecule #62: 40S ribosomal protein S11
+Macromolecule #63: 40S ribosomal protein S12
+Macromolecule #64: 40S ribosomal protein S13
+Macromolecule #65: Small ribosomal subunit protein uS11
+Macromolecule #66: 40S ribosomal protein S15
+Macromolecule #67: Small ribosomal subunit protein uS9
+Macromolecule #68: 40S ribosomal protein S17
+Macromolecule #69: 40S ribosomal protein S18
+Macromolecule #70: Small ribosomal subunit protein eS19
+Macromolecule #71: 40S ribosomal protein S20
+Macromolecule #72: eS21
+Macromolecule #73: 40S ribosomal protein S15a
+Macromolecule #74: 40S ribosomal protein S23
+Macromolecule #75: 40S ribosomal protein S24
+Macromolecule #76: 40S ribosomal protein S25
+Macromolecule #77: eS26
+Macromolecule #78: 40S ribosomal protein S27
+Macromolecule #79: 40S ribosomal protein S28
+Macromolecule #80: 40S ribosomal protein S29
+Macromolecule #81: 40S ribosomal protein S30
+Macromolecule #82: Elongation factor 1-alpha
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7 |
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| Grid | Model: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | FEI TALOS ARCTICA |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2 |
| Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
| Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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About Yorodumi



Keywords

Homo sapiens (human)
Authors
United States, 1 items
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Processing
FIELD EMISSION GUN


