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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | Mouse Ribosome POST translocation state | |||||||||
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Keywords | Translating Ribosomes / POST state / Mouse / Ba/F3 / Polysomes / RIBOSOME | |||||||||
| Function / homology | Function and homology informationRibosome Quality Control (RQC) complex extracts and degrades nascent peptide / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / TNFR1-mediated ceramide production / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / 5.8S rRNA binding / Protein hydroxylation / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of myoblast fusion / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A ...Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / TNFR1-mediated ceramide production / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / 5.8S rRNA binding / Protein hydroxylation / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of myoblast fusion / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / negative regulation of protein neddylation / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of expression of SLITs and ROBOs / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Alpha-protein kinase 1 signaling pathway / Pexophagy / Regulation of pyruvate metabolism / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Formation of a pool of free 40S subunits / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / SCF-beta-TrCP mediated degradation of Emi1 / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / SRP-dependent cotranslational protein targeting to membrane / p75NTR recruits signalling complexes / Interferon alpha/beta signaling / Negative regulation of MAPK pathway / Major pathway of rRNA processing in the nucleolus and cytosol / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / E3 ubiquitin ligases ubiquitinate target proteins / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Ubiquitin-dependent degradation of Cyclin D / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / Downregulation of ERBB2 signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Dual incision in TC-NER / Oncogene Induced Senescence / Degradation of CRY and PER proteins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / TNFR1-induced NF-kappa-B signaling pathway / HDR through Homologous Recombination (HRR) / Gap-filling DNA repair synthesis and ligation in TC-NER / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Metalloprotease DUBs / Formation of Incision Complex in GG-NER / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of BACH1 activity / EGFR downregulation / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / mammalian oogenesis stage / Degradation of AXIN / Protein methylation / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.78 Å | |||||||||
Authors | Santo PE / Astier A / Plisson-Chastang C | |||||||||
| Funding support | France, 1 items
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Citation | Journal: Hemasphere / Year: 2026Title: A RiboCancer cell line panel reveals that CLL-associated Rps15 mutations translationally rewire transcription through codon-specific tRNA accommodation defects. Authors: Anaïs Astier / Marino Caruso / Stijn Vereecke / Paulo E Santo / Coralie Capron / Carine Froment / Dana Rinaldi / David Cabrerizo Granados / Marine Leclercq / Jonathan Royaert / Jelle ...Authors: Anaïs Astier / Marino Caruso / Stijn Vereecke / Paulo E Santo / Coralie Capron / Carine Froment / Dana Rinaldi / David Cabrerizo Granados / Marine Leclercq / Jonathan Royaert / Jelle Verbeeck / Naomy Pasau / Laura Plassart / Daniele Pepe / Steven Verbruggen / Hermes Paraqindes / Simon Lebaron / Virginie Marcel / Sébastien Durand / Clément Chapat / Gerben Menschaert / Pierre Close / Francesca Rapino / Frédéric Catez / Julien Marcoux / Célia Plisson-Chastang / Kim De Keersmaecker / ![]() Abstract: Recurrent point mutations in ribosomal proteins (RPs) RPL10 and RPS15 are found in T-cell acute lymphoblastic leukemia (T-ALL) and chronic lymphocytic leukemia (CLL), respectively. Furthermore, ...Recurrent point mutations in ribosomal proteins (RPs) RPL10 and RPS15 are found in T-cell acute lymphoblastic leukemia (T-ALL) and chronic lymphocytic leukemia (CLL), respectively. Furthermore, deletions of RPL5, RPL11, and RPL22 are frequent in hematologic diseases such as Diamond Blackfan Anemia, T-ALL, multiple myeloma, and in a variety of solid tumors. Yet, the role of these RP defects in dysregulation of the ribosomal translation function remains poorly understood. We engineered an isogenic RiboCancer cell line library modeling the most recurrent RP defects in blood and solid cancers and characterized it by a multi-omics translatome analysis (proteome, Ribo-seq, and total RNA-seq) as well as RiboMethSeq. Within this RiboCancer panel, CLLassociated Rps15 mutations induced the strongest alterations in mRNA translation, affecting up to 10% of expressed genes. Cryo-electron microscopy revealed that these mutations destabilize the Rps15 C-terminus and affect the translation elongation cycle dynamics by deregulating accommodation of aminoacylated tRNAs at the ribosomal A-site. This accommodation defect showed specificity for 11 codons, explaining the reduced translation efficiency of genes with high presence of these codons in Rps15-mutant cells. Notably, these genes were enriched for epigenetic and transcriptional regulators such as transcription factor Runx3, resulting in downregulation of Runx3 target genes involved in immune regulation. By developing and characterizing a unique RiboCancer cell line panel, we mapped translational rewiring driven by the most frequent somatic RP mutations. We provide unprecedented mechanistic insights into translation defects induced by CLL-associated Rps15 mutations, and reveal an intriguing translation-based rewiring of transcription in CLL. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_53262.map.gz | 29.5 MB | EMDB map data format | |
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| Header (meta data) | emd-53262-v30.xml emd-53262.xml | 114.4 KB 114.4 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_53262_fsc.xml | 11 KB | Display | FSC data file |
| Images | emd_53262.png | 68.6 KB | ||
| Filedesc metadata | emd-53262.cif.gz | 21.8 KB | ||
| Others | emd_53262_additional_1.map.gz emd_53262_half_map_1.map.gz emd_53262_half_map_2.map.gz | 90.5 MB 90.8 MB 90.8 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-53262 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-53262 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9qohMC ![]() 9qqlC ![]() 9qqpC ![]() 9qsaC ![]() 9qwtC ![]() 9qzpC M: atomic model generated by this map C: citing same article ( |
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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_53262.map.gz / Format: CCP4 / Size: 115.9 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: 1.01 Å | ||||||||||||||||||||||||||||||||||||
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: #1
| File | emd_53262_additional_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_53262_half_map_1.map | ||||||||||||
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-Half map: #2
| File | emd_53262_half_map_2.map | ||||||||||||
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Sample components
+Entire : Elogating Ribosome in POST translocation state
+Supramolecule #1: Elogating Ribosome in POST translocation state
+Macromolecule #1: Large ribosomal subunit protein uL30
+Macromolecule #3: Small ribosomal subunit protein uS13
+Macromolecule #4: Large ribosomal subunit protein eL8
+Macromolecule #6: Small ribosomal subunit protein eS19
+Macromolecule #9: Large ribosomal subunit protein uL6
+Macromolecule #11: Small ribosomal subunit protein uS10
+Macromolecule #12: Large ribosomal subunit protein uL16
+Macromolecule #13: Large ribosomal subunit protein uL2
+Macromolecule #14: Small ribosomal subunit protein eS21
+Macromolecule #15: Large ribosomal subunit protein uL5
+Macromolecule #16: Large ribosomal subunit protein uL3
+Macromolecule #17: Small ribosomal subunit protein uS12
+Macromolecule #18: Large ribosomal subunit protein eL13
+Macromolecule #19: Large ribosomal subunit protein uL4
+Macromolecule #20: Small ribosomal subunit protein eS26
+Macromolecule #21: Large ribosomal subunit protein eL14
+Macromolecule #22: Large ribosomal subunit protein uL18
+Macromolecule #23: Small ribosomal subunit protein eS28
+Macromolecule #24: Large ribosomal subunit protein eL15
+Macromolecule #25: Large ribosomal subunit protein eL6
+Macromolecule #26: Small ribosomal subunit protein uS14
+Macromolecule #27: Large ribosomal subunit protein uL13
+Macromolecule #28: Small ribosomal subunit protein RACK1
+Macromolecule #29: Large ribosomal subunit protein uL22
+Macromolecule #30: Small ribosomal subunit protein uS5
+Macromolecule #31: Large ribosomal subunit protein eL18
+Macromolecule #32: Small ribosomal subunit protein eS6
+Macromolecule #33: Large ribosomal subunit protein uL1
+Macromolecule #34: Large ribosomal subunit protein eL19
+Macromolecule #35: Small ribosomal subunit protein uS4
+Macromolecule #36: Large ribosomal subunit protein eL20
+Macromolecule #37: Small ribosomal subunit protein eS12
+Macromolecule #38: Large ribosomal subunit protein eL21
+Macromolecule #39: Small ribosomal subunit protein uS15
+Macromolecule #40: Large ribosomal subunit protein eL22
+Macromolecule #41: Small ribosomal subunit protein uS11
+Macromolecule #42: Large ribosomal subunit protein uL14
+Macromolecule #43: Small ribosomal subunit protein uS8
+Macromolecule #44: Large ribosomal subunit protein eL24
+Macromolecule #45: Small ribosomal subunit protein eS24
+Macromolecule #46: Large ribosomal subunit protein uL23
+Macromolecule #47: Small ribosomal subunit protein eS25
+Macromolecule #48: Large ribosomal subunit protein uL24
+Macromolecule #49: Small ribosomal subunit protein eS27
+Macromolecule #50: Large ribosomal subunit protein eL27
+Macromolecule #51: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+Macromolecule #52: Large ribosomal subunit protein uL15
+Macromolecule #53: Ubiquitin-ribosomal protein eS31 fusion protein
+Macromolecule #54: Large ribosomal subunit protein eL29
+Macromolecule #55: Large ribosomal subunit protein eL30
+Macromolecule #56: Large ribosomal subunit protein eL31
+Macromolecule #57: Large ribosomal subunit protein eL32
+Macromolecule #58: Large ribosomal subunit protein eL33
+Macromolecule #59: Large ribosomal subunit protein eL34
+Macromolecule #60: Large ribosomal subunit protein uL29
+Macromolecule #61: Large ribosomal subunit protein eL36
+Macromolecule #62: Large ribosomal subunit protein eL37
+Macromolecule #63: Large ribosomal subunit protein eL38
+Macromolecule #64: Large ribosomal subunit protein eL39
+Macromolecule #65: Ubiquitin-ribosomal protein eL40 fusion protein
+Macromolecule #66: 60S ribosomal protein L41
+Macromolecule #67: Large ribosomal subunit protein eL42
+Macromolecule #68: Large ribosomal subunit protein eL43
+Macromolecule #69: Large ribosomal subunit protein eL28
+Macromolecule #71: Small ribosomal subunit protein uS2
+Macromolecule #72: 40S ribosomal protein S3a
+Macromolecule #73: Small ribosomal subunit protein uS3
+Macromolecule #74: Small ribosomal subunit protein eS4
+Macromolecule #75: Small ribosomal subunit protein uS7
+Macromolecule #76: Small ribosomal subunit protein eS7
+Macromolecule #77: Small ribosomal subunit protein eS8
+Macromolecule #78: Small ribosomal subunit protein eS10
+Macromolecule #79: Small ribosomal subunit protein uS17
+Macromolecule #80: Small ribosomal subunit protein uS19
+Macromolecule #81: Small ribosomal subunit protein uS9
+Macromolecule #82: Small ribosomal subunit protein eS17
+Macromolecule #83: Nascent protein chain
+Macromolecule #2: 28S ribosomal RNA
+Macromolecule #5: 5S ribosomal RNA
+Macromolecule #7: transfer RNA
+Macromolecule #8: messenger RNA
+Macromolecule #10: 5.8S ribosomal RNA
+Macromolecule #70: 18S ribosomal RNA
+Macromolecule #84: MAGNESIUM ION
+Macromolecule #85: ZINC ION
+Macromolecule #86: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 0.5 mg/mL | |||||||||||||||
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| Buffer | pH: 7.5 Component:
Details: 20 mM Hepes pH 7.5, 150 mM NaCl, 10 mM MgCl2, 1 mM DTT | |||||||||||||||
| Grid | Model: Quantifoil Active R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0003 kPa | |||||||||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 292 K / Instrument: LEICA EM GP | |||||||||||||||
| Details | RNA concentration was measured by nanordrop |
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Electron microscopy
| Microscope | FEI TALOS ARCTICA |
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| Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 7139 / Average electron dose: 45.0 e/Å2 |
| Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 100000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
| Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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| Details | Initial fitting was done using PDB ID 7LS1 in Chimera. Refmac and Phenix were used for Refine |
| Refinement | Space: REAL / Protocol: RIGID BODY FIT |
| Output model | ![]() PDB-9qoh: |
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Keywords
Authors
France, 1 items
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Z (Sec.)
Y (Row.)
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FIELD EMISSION GUN


