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Open data
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Basic information
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| Title | Structure of guinea pig ribosome with P/E-tRNA and mRNA | |||||||||||||||
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Keywords | Guinea pig ribosome / RIBOSOME | |||||||||||||||
| Function / homology | Function and homology informationtranslation at postsynapse / translation at presynapse / eukaryotic 80S initiation complex / axial mesoderm development / regulation of G1 to G0 transition / protein-DNA complex disassembly / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport ...translation at postsynapse / translation at presynapse / eukaryotic 80S initiation complex / axial mesoderm development / regulation of G1 to G0 transition / protein-DNA complex disassembly / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / G1 to G0 transition / cysteine-type endopeptidase activator activity involved in apoptotic process / neural crest cell differentiation / middle ear morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of phagocytosis / ion channel inhibitor activity / pigmentation / positive regulation of mitochondrial depolarization / cellular response to actinomycin D / BH3 domain binding / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein serine/threonine kinase inhibitor activity / negative regulation of ubiquitin-dependent protein catabolic process / ubiquitin ligase inhibitor activity / 90S preribosome / positive regulation of signal transduction by p53 class mediator / regulation of translational fidelity / phagocytic cup / positive regulation of intrinsic apoptotic signaling pathway / positive regulation of cell cycle / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / signaling adaptor activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / stress granule assembly / rescue of stalled cytosolic ribosome / SH2 domain binding / ossification / cyclin binding / protein kinase C binding / cellular response to leukemia inhibitory factor / skeletal system development / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / innate immune response in mucosa / mRNA 3'-UTR binding / negative regulation of smoothened signaling pathway / neural tube closure / cellular response to glucose stimulus / small-subunit processome / positive regulation of protein-containing complex assembly / sensory perception of sound / negative regulation of cell growth / receptor tyrosine kinase binding / maintenance of translational fidelity / mRNA 5'-UTR binding / cellular response to growth factor stimulus / transcription coactivator binding / response to virus / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of translation / large ribosomal subunit / antibacterial humoral response / presynapse / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / midbody / protein phosphatase binding / cytosolic large ribosomal subunit / killing of cells of another organism / defense response to Gram-negative bacterium / cytoplasmic translation / cell differentiation / regulation of cell cycle / postsynapse / rRNA binding / postsynaptic density / protein stabilization / positive regulation of cell migration / defense response to Gram-positive bacterium / structural constituent of ribosome / protein ubiquitination / ribosome / translation / ribonucleoprotein complex / negative regulation of gene expression / neuronal cell body / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding Similarity search - Function | |||||||||||||||
| Biological species | Cavia porcellus (domestic guinea pig) | |||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 4.7 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_72483.map.gz | 193.9 MB | EMDB map data format | |
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| Header (meta data) | emd-72483-v30.xml emd-72483.xml | 103.5 KB 103.5 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_72483_fsc.xml | 18.4 KB | Display | FSC data file |
| Images | emd_72483.png | 126 KB | ||
| Filedesc metadata | emd-72483.cif.gz | 19.8 KB | ||
| Others | emd_72483_additional_1.map.gz emd_72483_additional_2.map.gz emd_72483_half_map_1.map.gz emd_72483_half_map_2.map.gz | 221.4 MB 217.9 MB 194.7 MB 194.6 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-72483 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-72483 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9y4hMC ![]() 9y42C ![]() 9y44C ![]() 9y49C ![]() 9y4gC ![]() 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_72483.map.gz / Format: CCP4 / Size: 244.1 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: 0.98 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: DeepEMhancer sharpened map
| File | emd_72483_additional_1.map | ||||||||||||
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| Annotation | DeepEMhancer sharpened map | ||||||||||||
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| Density Histograms |
-Additional map: phenix sharpened map
| File | emd_72483_additional_2.map | ||||||||||||
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| Annotation | phenix sharpened map | ||||||||||||
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-Half map: #2
| File | emd_72483_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_72483_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Guinea Pig Ribosome
+Supramolecule #1: Guinea Pig Ribosome
+Macromolecule #1: 40S ribosomal protein S14
+Macromolecule #2: Small ribosomal subunit protein uS12
+Macromolecule #3: 40S ribosomal protein S13
+Macromolecule #4: Small ribosomal subunit protein uS17
+Macromolecule #5: Small ribosomal subunit protein eS1
+Macromolecule #6: 40S ribosomal protein SA
+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: FAU ubiquitin like and ribosomal protein S30 fusion
+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: Large ribosomal subunit protein eL24
+Macromolecule #21: Small ribosomal subunit protein RACK1
+Macromolecule #22: Small ribosomal subunit protein uS10
+Macromolecule #23: 40S ribosomal protein S10
+Macromolecule #24: Small ribosomal subunit protein uS13
+Macromolecule #25: Small ribosomal subunit protein uS14
+Macromolecule #26: Small ribosomal subunit protein eS17
+Macromolecule #27: 40S ribosomal protein S15
+Macromolecule #28: Small ribosomal subunit protein eS19
+Macromolecule #29: 40S ribosomal protein S25
+Macromolecule #30: 40S ribosomal protein S28
+Macromolecule #31: 40S ribosomal protein S3
+Macromolecule #32: Small ribosomal subunit protein uS7
+Macromolecule #33: Small ribosomal subunit protein uS9
+Macromolecule #34: 60S ribosomal protein L13a
+Macromolecule #35: 60S ribosomal protein L13
+Macromolecule #36: Large ribosomal subunit protein uL14
+Macromolecule #37: 60S ribosomal protein L14
+Macromolecule #38: 60S ribosomal protein L27a
+Macromolecule #39: Ribosomal protein L15
+Macromolecule #40: 60S ribosomal protein L10-like
+Macromolecule #41: 60S ribosomal protein L5
+Macromolecule #42: 60S ribosomal protein L18
+Macromolecule #43: Large ribosomal subunit protein uL2
+Macromolecule #44: 60S ribosomal protein L18a
+Macromolecule #45: Large ribosomal subunit protein eL21
+Macromolecule #46: 60S ribosomal protein L17
+Macromolecule #47: 60S ribosomal protein L22
+Macromolecule #48: 60S ribosomal protein L23a
+Macromolecule #49: Large ribosomal subunit protein uL24
+Macromolecule #50: 60S ribosomal protein L27
+Macromolecule #51: Large ribosomal subunit protein eL28
+Macromolecule #52: 60S ribosomal protein L35
+Macromolecule #53: 60S ribosomal protein L29
+Macromolecule #54: 60S ribosomal protein L3
+Macromolecule #55: 60S ribosomal protein L7
+Macromolecule #56: Large ribosomal subunit protein eL30
+Macromolecule #57: Large ribosomal subunit protein eL31
+Macromolecule #58: Ribosomal protein L32
+Macromolecule #59: 60S ribosomal protein L35a
+Macromolecule #60: Large ribosomal subunit protein eL34
+Macromolecule #61: 60S ribosomal protein L36
+Macromolecule #62: Ribosomal protein L37
+Macromolecule #63: Large ribosomal subunit protein eL38
+Macromolecule #64: 60S ribosomal protein L39
+Macromolecule #65: 60S ribosomal protein L4
+Macromolecule #66: Ubiquitin-ribosomal protein eL40 fusion protein
+Macromolecule #67: 60S ribosomal protein L41
+Macromolecule #68: Large ribosomal subunit protein eL43
+Macromolecule #69: Ribosomal protein L36a
+Macromolecule #70: Large ribosomal subunit protein uL5
+Macromolecule #71: 60S ribosomal protein L9
+Macromolecule #72: 60S ribosomal protein L6
+Macromolecule #73: 60S ribosomal protein L7a
+Macromolecule #19: 18S rRNA (1803-MER)
+Macromolecule #74: 28S ribosomal RNA
+Macromolecule #75: 5S ribosomal RNA
+Macromolecule #76: 5.8S ribosomal RNA
+Macromolecule #77: tRNA
+Macromolecule #78: mRNA
+Macromolecule #79: 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 R1.2/1.3 / Material: GOLD / Mesh: 300 / 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 | FEI TECNAI F30 |
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| Software | Name: Leginon |
| Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: INTEGRATING / Number real images: 3904 / 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: Tecnai F30 / Image courtesy: FEI Company |
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About Yorodumi




Keywords
Cavia porcellus (domestic guinea pig)
Authors
United States, 4 items
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Processing
FIELD EMISSION GUN



