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Yorodumi- EMDB-72469: Structure of naked mole-rat ribosome with P/E tRNA and eEF2 (rotated) -
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Open data
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Basic information
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| Title | Structure of naked mole-rat ribosome with P/E tRNA and eEF2 (rotated) | |||||||||||||||
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Keywords | Naked mole rat ribosome / RIBOSOME | |||||||||||||||
| Function / homology | Function and homology informationregulation of G1 to G0 transition / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of DNA repair / G1 to G0 transition / supercoiled DNA binding / NF-kappaB complex ...regulation of G1 to G0 transition / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of DNA repair / G1 to G0 transition / supercoiled DNA binding / NF-kappaB complex / neural crest cell differentiation / oxidized purine DNA binding / ubiquitin-like protein conjugating enzyme binding / protein kinase A binding / laminin receptor activity / cellular response to actinomycin D / positive regulation of T cell receptor signaling pathway / TOR signaling / positive regulation of activated T cell proliferation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of ubiquitin-dependent protein catabolic process / ubiquitin ligase inhibitor activity / 90S preribosome / positive regulation of signal transduction by p53 class mediator / protein-RNA complex assembly / spindle assembly / positive regulation of microtubule polymerization / positive regulation of cell cycle / laminin binding / rough endoplasmic reticulum / translation regulator activity / gastrulation / negative regulation of protein ubiquitination / Hsp70 protein binding / positive regulation of interleukin-2 production / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mRNA 3'-UTR binding / neural tube closure / small-subunit processome / Hsp90 protein binding / positive regulation of non-canonical NF-kappaB signal transduction / base-excision repair / mRNA 5'-UTR binding / transcription coactivator binding / response to virus / ruffle membrane / cellular response to hydrogen peroxide / cytoplasmic ribonucleoprotein granule / rRNA processing / kinase activity / cellular response to tumor necrosis factor / mitotic spindle / large ribosomal subunit / ribosome binding / cell body / ribosomal small subunit biogenesis / ribosomal small subunit assembly / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / microtubule binding / cytosolic large ribosomal subunit / DNA-binding transcription factor binding / cytoplasmic translation / mitochondrial inner membrane / negative regulation of translation / rRNA binding / postsynaptic density / protein stabilization / structural constituent of ribosome / positive regulation of apoptotic process / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / mRNA binding / apoptotic process / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of gene expression / centrosome / protein kinase binding / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm Similarity search - Function | |||||||||||||||
| Biological species | Heterocephalus glaber (naked mole-rat) | |||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 5.0 Å | |||||||||||||||
Authors | Gutierrez-Vargas C / De S / Maji S / Liu Z / Nieb M / Seluanov A / Gorbunova V / Frank J | |||||||||||||||
| Funding support | United States, 4 items
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Citation | Journal: Nucleic Acids Res / Year: 2026Title: Structures of naked mole-rat, tuco-tuco, and guinea pig ribosomes-is rRNA fragmentation linked to translational fidelity? Authors: Cristina Gutierrez-Vargas / Swastik De / Suvrajit Maji / Zheng Liu / Zhonghe Ke / Martina Nieß / Andrei Seluanov / Vera Gorbunova / Joachim Frank / ![]() Abstract: Ribosomes are central to protein synthesis in all organisms. In mammals, the ribosome functional core is highly conserved. Remarkably, two rodent species, the naked mole-rat (NMR) and tuco-tuco, ...Ribosomes are central to protein synthesis in all organisms. In mammals, the ribosome functional core is highly conserved. Remarkably, two rodent species, the naked mole-rat (NMR) and tuco-tuco, display fragmented 28S ribosomal RNA (rRNA), coupled with high translational fidelity and long lifespan. The unusual ribosomal architecture in the NMR and tuco-tuco has been speculated to be linked to high translational fidelity. Here, we show, by single-particle cryo-electron microscopy, that despite the fragmentation of their rRNA, NMR and tuco-tuco ribosomes retain their core functional architecture. Compared to ribosomes of the guinea pig, a phylogenetically related rodent without 28S rRNA fragmentation, ribosomes of NMR and tuco-tuco exhibit poorly resolved density for certain expansion segments. In contrast, the structure of the guinea pig ribosome shows high similarity to the human ribosome. Enhanced translational fidelity in the NMR and tuco-tuco may stem from subtle, allosteric effects in dynamics, linked to rRNA fragmentation. | |||||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_72469.map.gz | 257.8 MB | EMDB map data format | |
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| Header (meta data) | emd-72469-v30.xml emd-72469.xml | 107.7 KB 107.7 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_72469_fsc.xml | 20.2 KB | Display | FSC data file |
| Images | emd_72469.png | 126 KB | ||
| Filedesc metadata | emd-72469.cif.gz | 20.6 KB | ||
| Others | emd_72469_additional_1.map.gz emd_72469_half_map_1.map.gz emd_72469_half_map_2.map.gz | 299.2 MB 258.8 MB 258.8 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-72469 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-72469 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9y42MC ![]() 9y44C ![]() 9y49C ![]() 9y4gC ![]() 9y4hC ![]() 9zrgC 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_72469.map.gz / Format: CCP4 / Size: 325 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: 1.045 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: phenix sharpened map
| File | emd_72469_additional_1.map | ||||||||||||
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| Annotation | phenix sharpened map | ||||||||||||
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| Density Histograms |
-Half map: #2
| File | emd_72469_half_map_1.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
-Half map: #1
| File | emd_72469_half_map_2.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : Naked mole-rat ribosome
+Supramolecule #1: Naked mole-rat ribosome
+Macromolecule #1: Large ribosomal subunit protein uL2
+Macromolecule #2: 60S ribosomal protein L3
+Macromolecule #3: Large ribosomal subunit protein uL4
+Macromolecule #4: Large ribosomal subunit protein eL24
+Macromolecule #5: Large ribosomal subunit protein uL18
+Macromolecule #6: 60S ribosomal protein L6
+Macromolecule #7: 60S ribosomal protein L7
+Macromolecule #8: 60S ribosomal protein L7a
+Macromolecule #9: 60S ribosomal protein L9
+Macromolecule #10: 60S ribosomal protein L10
+Macromolecule #11: Large ribosomal subunit protein uL5
+Macromolecule #12: 60S ribosomal protein L13
+Macromolecule #13: Large ribosomal subunit protein eL14
+Macromolecule #14: Ribosomal protein L15
+Macromolecule #15: 60S ribosomal protein L13a
+Macromolecule #16: 60S ribosomal protein L17
+Macromolecule #17: 60S ribosomal protein L18
+Macromolecule #18: Large ribosomal subunit protein eL20
+Macromolecule #19: Large ribosomal subunit protein eL21
+Macromolecule #20: 60S ribosomal protein L22
+Macromolecule #21: Large ribosomal subunit protein uL14
+Macromolecule #22: Ribosomal protein L19
+Macromolecule #23: Large ribosomal subunit protein uL23
+Macromolecule #24: 60S ribosomal protein L26
+Macromolecule #25: 60S ribosomal protein L27
+Macromolecule #26: 60S ribosomal protein L27a
+Macromolecule #27: 60S ribosomal protein L29
+Macromolecule #28: Large ribosomal subunit protein eL31
+Macromolecule #29: 60S ribosomal protein L32
+Macromolecule #30: Large ribosomal subunit protein eL33
+Macromolecule #31: Large ribosomal subunit protein eL34
+Macromolecule #32: Large ribosomal subunit protein uL29
+Macromolecule #33: 60S ribosomal protein L36
+Macromolecule #34: Ribosomal protein L37
+Macromolecule #35: Large ribosomal subunit protein eL38
+Macromolecule #36: 60S ribosomal protein L39
+Macromolecule #37: Ubiquitin-ribosomal protein eL40 fusion protein
+Macromolecule #38: 60S ribosomal protein L41
+Macromolecule #39: 60S ribosomal protein L36a
+Macromolecule #40: Large ribosomal subunit protein eL43
+Macromolecule #41: Large ribosomal subunit protein eL28
+Macromolecule #42: 60S acidic ribosomal protein P0
+Macromolecule #43: 60S ribosomal protein L12
+Macromolecule #44: Large ribosomal subunit protein eL30
+Macromolecule #45: 40S ribosomal protein S27
+Macromolecule #46: 40S ribosomal protein S30
+Macromolecule #47: 40S ribosomal protein S26
+Macromolecule #48: 40S ribosomal protein S2
+Macromolecule #49: 40S ribosomal protein S4, X isoform
+Macromolecule #50: 40S ribosomal protein S6
+Macromolecule #51: 40S ribosomal protein S7
+Macromolecule #52: 40S ribosomal protein S8
+Macromolecule #53: Small ribosomal subunit protein uS4
+Macromolecule #54: Small ribosomal subunit protein uS17
+Macromolecule #55: Small ribosomal subunit protein uS15
+Macromolecule #56: 40S ribosomal protein S21
+Macromolecule #57: Small ribosomal subunit protein uS8
+Macromolecule #58: Small ribosomal subunit protein uS12
+Macromolecule #59: 40S ribosomal protein S24
+Macromolecule #60: 40S ribosomal protein S28
+Macromolecule #61: Ubiquitin-ribosomal protein eS31 fusion protein
+Macromolecule #62: Small ribosomal subunit protein RACK1
+Macromolecule #63: Small ribosomal subunit protein uS14
+Macromolecule #64: Small ribosomal subunit protein uS2
+Macromolecule #65: Small ribosomal subunit protein uS3
+Macromolecule #66: Small ribosomal subunit protein uS7
+Macromolecule #67: Small ribosomal subunit protein eS10
+Macromolecule #68: 40S ribosomal protein S12
+Macromolecule #69: 40S ribosomal protein S15
+Macromolecule #70: Small ribosomal subunit protein uS9
+Macromolecule #71: Small ribosomal subunit protein uS13
+Macromolecule #72: Small ribosomal subunit protein eS19
+Macromolecule #73: 40S ribosomal protein S20
+Macromolecule #74: 40S ribosomal protein S25
+Macromolecule #75: eEF2
+Macromolecule #82: 40S ribosomal protein S3a
+Macromolecule #83: 40S ribosomal protein S14
+Macromolecule #84: Small ribosomal subunit protein eS17
+Macromolecule #76: P/E tRNA (77-MER)
+Macromolecule #77: LSU alpha rRNA
+Macromolecule #78: 5S ribosomal RNA
+Macromolecule #79: 5.8S ribosomal RNA
+Macromolecule #80: 18S ribosomal RNA
+Macromolecule #81: LSU beta rRNA
+Macromolecule #85: MAGNESIUM ION
+Macromolecule #86: ZINC ION
+Macromolecule #87: 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
| Buffer | pH: 7.4 Component:
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| Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number real images: 6147 / Average electron dose: 40.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
| Initial model |
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| Refinement | Protocol: RIGID BODY FIT | |||||||||
| Output model | ![]() PDB-9y42: |
Movie
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About Yorodumi



Keywords
Heterocephalus glaber (naked mole-rat)
Authors
United States, 4 items
Citation




















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FIELD EMISSION GUN




