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Open data
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Basic information
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| Title | Structure of naked mole-rat ribosome (non-rotated) | ||||||||||||
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Keywords | Naked mole rat ribosome / RIBOSOME | ||||||||||||
| Function / homology | Function and homology informationregulation of G1 to G0 transition / protein-DNA complex disassembly / G1 to G0 transition / neural crest cell differentiation / laminin receptor activity / cellular response to actinomycin D / TOR signaling / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of ubiquitin-dependent protein catabolic process / ubiquitin ligase inhibitor activity ...regulation of G1 to G0 transition / protein-DNA complex disassembly / G1 to G0 transition / neural crest cell differentiation / laminin receptor activity / cellular response to actinomycin D / TOR signaling / 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 / positive regulation of cell cycle / laminin binding / rough endoplasmic reticulum / translation regulator activity / gastrulation / cytosolic ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / innate immune response in mucosa / mRNA 3'-UTR binding / neural tube closure / small-subunit processome / mRNA 5'-UTR binding / transcription coactivator binding / response to virus / cytoplasmic ribonucleoprotein granule / rRNA processing / kinase activity / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit / antibacterial humoral response / ribosome binding / cell body / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / rRNA binding / protein stabilization / defense response to Gram-positive bacterium / structural constituent of ribosome / positive regulation of apoptotic process / ribosome / translation / ribonucleoprotein complex / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of gene expression / centrosome / protein kinase binding / negative regulation of apoptotic process / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / extracellular space / RNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
| Biological species | Heterocephalus glaber (naked mole-rat) | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Gutierrez-Vargas C / De S / Maji S / Liu Z / Nieb M / Seluanov A / Gorbunova V / Frank J | ||||||||||||
| Funding support | United States, 3 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_74615.map.gz | 224.9 MB | EMDB map data format | |
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| Header (meta data) | emd-74615-v30.xml emd-74615.xml | 122.3 KB 122.3 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_74615_fsc.xml | 14.9 KB | Display | FSC data file |
| Images | emd_74615.png | 124.8 KB | ||
| Filedesc metadata | emd-74615.cif.gz | 20.3 KB | ||
| Others | emd_74615_additional_1.map.gz emd_74615_half_map_1.map.gz emd_74615_half_map_2.map.gz | 254 MB 224.6 MB 224.5 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-74615 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-74615 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9zrgMC ![]() 9y42C ![]() 9y44C ![]() 9y49C ![]() 9y4gC ![]() 9y4hC 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_74615.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
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| Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||||||||||||||||||
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: #1
| File | emd_74615_additional_1.map | ||||||||||||
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-Half map: #2
| File | emd_74615_half_map_1.map | ||||||||||||
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-Half map: #1
| File | emd_74615_half_map_2.map | ||||||||||||
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Sample components
+Entire : Naked mole-rat Ribosome
+Supramolecule #1: Naked mole-rat Ribosome
+Macromolecule #1: 40S ribosomal protein S14
+Macromolecule #2: Small ribosomal subunit protein uS12
+Macromolecule #3: Small ribosomal subunit protein uS15
+Macromolecule #4: Small ribosomal subunit protein uS17
+Macromolecule #5: Small ribosomal subunit protein eS1
+Macromolecule #6: Small ribosomal subunit protein uS2
+Macromolecule #7: 40S ribosomal protein S21
+Macromolecule #8: 40S ribosomal protein S24
+Macromolecule #9: 40S ribosomal protein S26
+Macromolecule #10: 40S ribosomal protein S27
+Macromolecule #11: Ubiquitin-like protein FUBI
+Macromolecule #12: Small ribosomal subunit protein uS4
+Macromolecule #13: 40S ribosomal protein S4, X isoform
+Macromolecule #14: 40S ribosomal protein S2
+Macromolecule #15: 40S ribosomal protein S6
+Macromolecule #16: 40S ribosomal protein S7
+Macromolecule #17: Small ribosomal subunit protein uS8
+Macromolecule #18: 40S ribosomal protein S8
+Macromolecule #20: 60S ribosomal protein L19
+Macromolecule #21: Large ribosomal subunit protein eL24
+Macromolecule #22: Small ribosomal subunit protein RACK1
+Macromolecule #23: 40S ribosomal protein S20
+Macromolecule #24: Small ribosomal subunit protein eS10
+Macromolecule #25: 40S ribosomal protein S12
+Macromolecule #26: Small ribosomal subunit protein uS13
+Macromolecule #27: Small ribosomal subunit protein uS14
+Macromolecule #28: Small ribosomal subunit protein eS17
+Macromolecule #29: 40S ribosomal protein S15
+Macromolecule #30: Small ribosomal subunit protein eS19
+Macromolecule #31: 40S ribosomal protein S25
+Macromolecule #32: 40S ribosomal protein S28
+Macromolecule #33: 40S ribosomal protein S3
+Macromolecule #34: Ubiquitin-ribosomal protein eS31 fusion protein
+Macromolecule #35: Small ribosomal subunit protein uS7
+Macromolecule #36: Small ribosomal subunit protein uS9
+Macromolecule #37: 60S ribosomal protein L10a
+Macromolecule #38: 60S ribosomal protein L13a
+Macromolecule #39: 60S ribosomal protein L13
+Macromolecule #40: Large ribosomal subunit protein uL14
+Macromolecule #41: 60S ribosomal protein L14
+Macromolecule #42: 60S ribosomal protein L27a
+Macromolecule #43: Ribosomal protein L15
+Macromolecule #44: 60S ribosomal protein L10-like
+Macromolecule #45: 60S ribosomal protein L5
+Macromolecule #46: 60S ribosomal protein L18
+Macromolecule #47: Large ribosomal subunit protein uL2
+Macromolecule #48: 60S ribosomal protein L18a
+Macromolecule #49: Large ribosomal subunit protein eL21
+Macromolecule #50: 60S ribosomal protein L17
+Macromolecule #51: Large ribosomal subunit protein eL22
+Macromolecule #52: Large ribosomal subunit protein uL23
+Macromolecule #53: 60S ribosomal protein L26
+Macromolecule #54: 60S ribosomal protein L27
+Macromolecule #55: 60S ribosomal protein L28
+Macromolecule #56: 60S ribosomal protein L35
+Macromolecule #57: Large ribosomal subunit protein eL29
+Macromolecule #58: 60S ribosomal protein L3
+Macromolecule #59: 60S ribosomal protein L7
+Macromolecule #60: 60S ribosomal protein L30
+Macromolecule #61: Large ribosomal subunit protein eL31
+Macromolecule #62: 60S ribosomal protein L32
+Macromolecule #63: 60S ribosomal protein L35a
+Macromolecule #64: Large ribosomal subunit protein eL34
+Macromolecule #65: 60S ribosomal protein L36
+Macromolecule #66: Ribosomal protein L37
+Macromolecule #67: Large ribosomal subunit protein eL38
+Macromolecule #68: Large ribosomal subunit protein eL39
+Macromolecule #69: 60S ribosomal protein L4
+Macromolecule #70: Ubiquitin-ribosomal protein eL40 fusion protein
+Macromolecule #71: 60S ribosomal protein L41
+Macromolecule #72: Large ribosomal subunit protein eL43
+Macromolecule #73: 60S ribosomal protein L36a
+Macromolecule #74: Large ribosomal subunit protein uL5
+Macromolecule #75: 60S ribosomal protein L9
+Macromolecule #76: 60S ribosomal protein L6
+Macromolecule #77: 60S ribosomal protein L7a
+Macromolecule #19: 18S ribosomal RNA
+Macromolecule #78: 28S ribosomal RNA
+Macromolecule #79: 5S ribosomal RNA
+Macromolecule #80: 5.8S ribosomal RNA
+Macromolecule #81: E-tRNA
-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-PROPANE / 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 |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi




Keywords
Heterocephalus glaber (naked mole-rat)
Authors
United States, 3 items
Citation

















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Processing
FIELD EMISSION GUN


