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Yorodumi- EMDB-44464: 80S ribosome bound with angiogenin and complex of eEF1A and Ala-t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44464 | |||||||||
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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 | |||||||||
Sample |
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Keywords | Angiogenin / RNase / RIBOSOME | |||||||||
Function / homology | Function and homology information Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / melatonin binding / HSF1 activation / cell communication ...Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / melatonin binding / HSF1 activation / cell communication / tRNA export from nucleus / ribosomal subunit / negative regulation of formation of translation preinitiation complex / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / fungal-type vacuole membrane / Adherens junctions interactions / Protein methylation / GAIT complex / oocyte maturation / regulation of G1 to G0 transition / exit from mitosis / 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 / retinal ganglion cell axon guidance / mammalian oogenesis stage / homeostatic process / G1 to G0 transition / activation-induced cell death of T cells / macrophage chemotaxis / lung morphogenesis / rRNA transcription / actin filament bundle assembly / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / translational elongation / basement membrane / 90S preribosome / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / RNA nuclease activity / protein-RNA complex assembly / erythrocyte development / translation elongation factor activity / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal small subunit export from nucleus / translation regulator activity / positive regulation of phosphorylation / ovarian follicle development / rough endoplasmic reticulum / 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) / gastrulation / MDM2/MDM4 family protein binding / maturation of LSU-rRNA / positive regulation of endothelial cell proliferation / Neutrophil degranulation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cytosolic ribosome / RNA endonuclease activity / activation of protein kinase B activity / actin filament polymerization / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / response to hormone / negative regulation of protein phosphorylation / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / positive regulation of translation / small-subunit processome / positive regulation of protein secretion / protein kinase C binding / negative regulation of smooth muscle cell proliferation / positive regulation of apoptotic signaling pathway / negative regulation of protein kinase activity / peptide binding / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / cellular response to type II interferon / mRNA 5'-UTR binding / transcription coactivator binding / spindle / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / rRNA processing / GDP binding / ribosomal small subunit biogenesis / actin filament binding / antimicrobial humoral immune response mediated by antimicrobial peptide / rhythmic process Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Escherichia coli (E. coli) / Homo sapiens (human) / Saccharomyces cerevisiae (brewer's yeast) | |||||||||
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: 2024 Title: 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
Supplemental images |
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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 | 39.8 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 (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-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 |
-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 |
-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 |
-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 |