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Yorodumi- EMDB-33329: High resolution cry-EM structure of the human 80S ribosome from S... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33329 | |||||||||
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Title | High resolution cry-EM structure of the human 80S ribosome from SNORD127+/+ Kasumi-1 cells | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / protein tyrosine kinase inhibitor activity / axial mesoderm development / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair ...eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / protein tyrosine kinase inhibitor activity / axial mesoderm development / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / ribosomal protein import into nucleus / positive regulation of respiratory burst involved in inflammatory response / negative regulation of formation of translation preinitiation complex / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / positive regulation of endodeoxyribonuclease activity / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / GAIT complex / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / oxidized purine DNA binding / NF-kappaB complex / middle ear morphogenesis / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / A band / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of G1 to G0 transition / exit from mitosis / laminin receptor activity / pigmentation / 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 / protein kinase A binding / optic nerve development / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / retinal ganglion cell axon guidance / positive regulation of mitochondrial depolarization / mammalian oogenesis stage / homeostatic process / G1 to G0 transition / activation-induced cell death of T cells / lung morphogenesis / positive regulation of T cell receptor signaling pathway / macrophage chemotaxis / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / iron-sulfur cluster binding / monocyte chemotaxis / positive regulation of activated T cell proliferation / Protein hydroxylation / regulation of cell division / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / blastocyst development / phagocytic cup / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein localization to nucleus / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / 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 / regulation of translational fidelity / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Cheng J / Beckmann R | |||||||||
Funding support | 1 items
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Citation | Journal: Cancer Discov / Year: 2023 Title: A Dynamic rRNA Ribomethylome Drives Stemness in Acute Myeloid Leukemia. Authors: Fengbiao Zhou / Nesrine Aroua / Yi Liu / Christian Rohde / Jingdong Cheng / Anna-Katharina Wirth / Daria Fijalkowska / Stefanie Göllner / Michelle Lotze / Haiyang Yun / Xiaobing Yu / ...Authors: Fengbiao Zhou / Nesrine Aroua / Yi Liu / Christian Rohde / Jingdong Cheng / Anna-Katharina Wirth / Daria Fijalkowska / Stefanie Göllner / Michelle Lotze / Haiyang Yun / Xiaobing Yu / Caroline Pabst / Tim Sauer / Thomas Oellerich / Hubert Serve / Christoph Röllig / Martin Bornhäuser / Christian Thiede / Claudia Baldus / Michaela Frye / Simon Raffel / Jeroen Krijgsveld / Irmela Jeremias / Roland Beckmann / Andreas Trumpp / Carsten Müller-Tidow / Abstract: The development and regulation of malignant self-renewal remain unresolved issues. Here, we provide biochemical, genetic, and functional evidence that dynamics in ribosomal RNA (rRNA) 2'-O- ...The development and regulation of malignant self-renewal remain unresolved issues. Here, we provide biochemical, genetic, and functional evidence that dynamics in ribosomal RNA (rRNA) 2'-O-methylation regulate leukemia stem cell (LSC) activity in vivo. A comprehensive analysis of the rRNA 2'-O-methylation landscape of 94 patients with acute myeloid leukemia (AML) revealed dynamic 2'-O-methylation specifically at exterior sites of ribosomes. The rRNA 2'-O-methylation pattern is closely associated with AML development stage and LSC gene expression signature. Forced expression of the 2'-O-methyltransferase fibrillarin (FBL) induced an AML stem cell phenotype and enabled engraftment of non-LSC leukemia cells in NSG mice. Enhanced 2'-O-methylation redirected the ribosome translation program toward amino acid transporter mRNAs enriched in optimal codons and subsequently increased intracellular amino acid levels. Methylation at the single site 18S-guanosine 1447 was instrumental for LSC activity. Collectively, our work demonstrates that dynamic 2'-O-methylation at specific sites on rRNAs shifts translational preferences and controls AML LSC self-renewal. SIGNIFICANCE: We establish the complete rRNA 2'-O-methylation landscape in human AML. Plasticity of rRNA 2'-O-methylation shifts protein translation toward an LSC phenotype. This dynamic process ...SIGNIFICANCE: We establish the complete rRNA 2'-O-methylation landscape in human AML. Plasticity of rRNA 2'-O-methylation shifts protein translation toward an LSC phenotype. This dynamic process constitutes a novel concept of how cancers reprogram cell fate and function. This article is highlighted in the In This Issue feature, p. 247. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33329.map.gz | 157.9 MB | EMDB map data format | |
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Header (meta data) | emd-33329-v30.xml emd-33329.xml | 95.5 KB 95.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33329_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_33329.png | 236.9 KB | ||
Others | emd_33329_additional_1.map.gz emd_33329_half_map_1.map.gz emd_33329_half_map_2.map.gz | 15.8 MB 225.2 MB 225.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33329 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33329 | HTTPS FTP |
-Validation report
Summary document | emd_33329_validation.pdf.gz | 1005.8 KB | Display | EMDB validaton report |
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Full document | emd_33329_full_validation.pdf.gz | 1005.4 KB | Display | |
Data in XML | emd_33329_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | emd_33329_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33329 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33329 | HTTPS FTP |
-Related structure data
Related structure data | 7xnxMC 7xnyC M: atomic model generated by this map C: citing same article (ref.) |
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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_33329.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_33329_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33329_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33329_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : ribosome
+Supramolecule #1: ribosome
+Macromolecule #1: 28S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 5.8S rRNA
+Macromolecule #45: 18S rRNA
+Macromolecule #79: tRNA
+Macromolecule #4: 60S ribosomal protein L8
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4
+Macromolecule #7: 60S ribosomal protein L5
+Macromolecule #8: 60S ribosomal protein L6
+Macromolecule #9: 60S ribosomal protein L7
+Macromolecule #10: 60S ribosomal protein L7a
+Macromolecule #11: 60S ribosomal protein L9
+Macromolecule #12: Ribosomal protein L10 isoform A
+Macromolecule #13: 60S ribosomal protein L11
+Macromolecule #14: 60S ribosomal protein L13
+Macromolecule #15: 60S ribosomal protein L14
+Macromolecule #16: 60S ribosomal protein L15
+Macromolecule #17: 60S ribosomal protein L13a
+Macromolecule #18: 60S ribosomal protein L17
+Macromolecule #19: 60S ribosomal protein L18
+Macromolecule #20: 60S ribosomal protein L19
+Macromolecule #21: 60S ribosomal protein L18a
+Macromolecule #22: 60S ribosomal protein L21
+Macromolecule #23: 60S ribosomal protein L22
+Macromolecule #24: 60S ribosomal protein L23
+Macromolecule #25: 60S ribosomal protein L24
+Macromolecule #26: 60S ribosomal protein L23a
+Macromolecule #27: 60S ribosomal protein L26
+Macromolecule #28: 60S ribosomal protein L27
+Macromolecule #29: 60S ribosomal protein L29
+Macromolecule #30: 60S ribosomal protein L30
+Macromolecule #31: 60S ribosomal protein L31
+Macromolecule #32: 60S ribosomal protein L32
+Macromolecule #33: 60S ribosomal protein L35a
+Macromolecule #34: 60S ribosomal protein L34
+Macromolecule #35: 60S ribosomal protein L35
+Macromolecule #36: 60S ribosomal protein L36
+Macromolecule #37: 60S ribosomal protein L37
+Macromolecule #38: 60S ribosomal protein L38
+Macromolecule #39: 60S ribosomal protein L39
+Macromolecule #40: Ubiquitin-60S ribosomal protein L40
+Macromolecule #41: 60S ribosomal protein L41
+Macromolecule #42: 60S ribosomal protein L36a
+Macromolecule #43: 60S ribosomal protein L37a
+Macromolecule #44: 60S ribosomal protein L28
+Macromolecule #46: 40S ribosomal protein SA
+Macromolecule #47: 40S ribosomal protein S3a
+Macromolecule #48: 40S ribosomal protein S3
+Macromolecule #49: 40S ribosomal protein S4, X isoform
+Macromolecule #50: 40S ribosomal protein S5
+Macromolecule #51: 40S ribosomal protein S7
+Macromolecule #52: 40S ribosomal protein S8
+Macromolecule #53: 40S ribosomal protein S10
+Macromolecule #54: 40S ribosomal protein S11
+Macromolecule #55: 40S ribosomal protein S15
+Macromolecule #56: 40S ribosomal protein S16
+Macromolecule #57: 40S ribosomal protein S17
+Macromolecule #58: 40S ribosomal protein S18
+Macromolecule #59: 40S ribosomal protein S19
+Macromolecule #60: 40S ribosomal protein S20
+Macromolecule #61: 40S ribosomal protein S21
+Macromolecule #62: 40S ribosomal protein S23
+Macromolecule #63: 40S ribosomal protein S26
+Macromolecule #64: 40S ribosomal protein S28
+Macromolecule #65: 40S ribosomal protein S29
+Macromolecule #66: Receptor of activated protein C kinase 1
+Macromolecule #67: 40S ribosomal protein S2
+Macromolecule #68: 40S ribosomal protein S6
+Macromolecule #69: 40S ribosomal protein S9
+Macromolecule #70: 40S ribosomal protein S12
+Macromolecule #71: 40S ribosomal protein S13
+Macromolecule #72: 40S ribosomal protein S14
+Macromolecule #73: 40S ribosomal protein S15a
+Macromolecule #74: 40S ribosomal protein S24
+Macromolecule #75: 40S ribosomal protein S25
+Macromolecule #76: 40S ribosomal protein S27
+Macromolecule #77: 40S ribosomal protein S30
+Macromolecule #78: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #80: MAGNESIUM ION
+Macromolecule #81: POTASSIUM ION
+Macromolecule #82: ZINC ION
+Macromolecule #83: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |