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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 / alpha-aminoacyl-tRNA binding / eukaryotic translation elongation factor 1 complex / angiogenin-PRI complex / tRNA-specific ribonuclease activity / negative regulation of translation in response to stress / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / melatonin binding / HSF1 activation / tRNA decay ...Eukaryotic Translation Elongation / alpha-aminoacyl-tRNA binding / eukaryotic translation elongation factor 1 complex / angiogenin-PRI complex / tRNA-specific ribonuclease activity / negative regulation of translation in response to stress / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / melatonin binding / HSF1 activation / tRNA decay / signaling / oocyte maturation / homeostatic process / cell communication / hematopoietic stem cell proliferation / tRNA export from nucleus / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / protein-RNA complex assembly / fungal-type vacuole membrane / Protein methylation / rRNA transcription / Adherens junctions interactions / regulation of translation involved in cellular response to UV / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / basement membrane / negative regulation of protein phosphorylation / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of phosphorylation / actin filament bundle assembly / RNA nuclease activity / translational elongation / translation elongation factor activity / endocytic vesicle / placenta development / ubiquitin ligase inhibitor activity / 90S preribosome / positive regulation of signal transduction by p53 class mediator / negative regulation of protein kinase activity / phagocytic cup / positive regulation of endothelial cell proliferation / negative regulation of ubiquitin-dependent protein catabolic process / actin filament polymerization / peptide binding / Neutrophil degranulation / RNA endonuclease activity / translation regulator activity / response to hormone / ribosomal small subunit export from nucleus / rough endoplasmic reticulum / ovarian follicle development / positive regulation of apoptotic signaling pathway / MDM2/MDM4 family protein binding / cellular response to amino acid starvation / positive regulation of protein secretion / stress granule assembly / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / ribosomal large subunit biogenesis / negative regulation of smooth muscle cell proliferation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA damage response, signal transduction by p53 class mediator / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / positive regulation of translation / small-subunit processome / cellular response to gamma radiation / spindle / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / mRNA 5'-UTR binding / transcription coactivator binding / angiogenesis / rRNA processing / actin filament binding / cytosolic ribosome / heparin binding / GDP binding / glucose homeostasis / cell migration / endonuclease activity / actin binding / large ribosomal subunit / ribosomal small subunit assembly / growth cone / ribosome binding / ribosomal small subunit biogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / antibacterial humoral response / response to hypoxia / cytoskeleton / cytosolic large ribosomal subunit / innate immune response / perikaryon 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. | |||||||||
| History |
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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 | https://data.pdbj.org/pub/emdb/structures/EMD-44464 ftp://data.pdbj.org/pub/emdb/structures/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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Y (Row.)
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Processing
FIELD EMISSION GUN


