+Open data
-Basic information
Entry | Database: PDB / ID: 8p60 | ||||||
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Title | Spraguea lophii ribosome dimer | ||||||
Components |
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Keywords | RIBOSOME / Microsporidia | ||||||
Function / homology | Function and homology information translation regulator activity / cytosolic ribosome / ribosome binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome ...translation regulator activity / cytosolic ribosome / ribosome binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / zinc ion binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Spraguea lophii 42_110 (fungus) | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 14.3 Å | ||||||
Authors | Gil Diez, P. / McLaren, M. / Isupov, M.N. / Daum, B. / Conners, R. / Williams, B. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Microbiol / Year: 2023 Title: CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state. Authors: Mathew McLaren / Rebecca Conners / Michail N Isupov / Patricia Gil-Díez / Lavinia Gambelli / Vicki A M Gold / Andreas Walter / Sean R Connell / Bryony Williams / Bertram Daum / Abstract: Translational control is an essential process for the cell to adapt to varying physiological or environmental conditions. To survive adverse conditions such as low nutrient levels, translation can be ...Translational control is an essential process for the cell to adapt to varying physiological or environmental conditions. To survive adverse conditions such as low nutrient levels, translation can be shut down almost entirely by inhibiting ribosomal function. Here we investigated eukaryotic hibernating ribosomes from the microsporidian parasite Spraguea lophii in situ by a combination of electron cryo-tomography and single-particle electron cryo-microscopy. We show that microsporidian spores contain hibernating ribosomes that are locked in a dimeric (100S) state, which is formed by a unique dimerization mechanism involving the beak region. The ribosomes within the dimer are fully assembled, suggesting that they are ready to be activated once the host cell is invaded. This study provides structural evidence for dimerization acting as a mechanism for ribosomal hibernation in microsporidia, and therefore demonstrates that eukaryotes utilize this mechanism in translational control. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p60.cif.gz | 7.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8p60.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8p60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/8p60 ftp://data.pdbj.org/pub/pdb/validation_reports/p6/8p60 | HTTPS FTP |
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-Related structure data
Related structure data | 17457MC 8p5dC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 6 molecules L50K50L70K70S60R60
#1: RNA chain | Mass: 849039.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: ...Details: CCACACACAAGGGAUCGUUUGGCUCCUGGGACGAGGAAGGGCGCAGCAGAGAGCGAUAUGUGUGGGAGCAGCAAGCAAUGACCACACGUCCCCGAAUACAGCAUAGUGCUGGAGUACUCCUUGGAAUUAAGCAUAUGAGUAAAGGAAGGAAAAGAAACUAACGAGGAUUCCCGUAGUAGCGGCGAGUGAACAGGGAACAGUCCAACAGUGUAAUUCUCAAAUGAGAAGUUGUCAAAAGGAAGAAGAUGUGAAUCAGAAAGAAAAGCUGAACGAUACAGGGUGAUAGUCCCGUAGUGUCUUCUUACAUACGGUGAGUAGCUGUGCUCGGUAAUGCACAGUGAAGAGGUGGCAGUGUGCAUCUAAGACUAAAUACAACAGGAGACCGAUAGCAAAGAAGUAGGUUGACCGAAAACAUCUAAGUGAAAUUGUGUGUGGACCCGAAUGGAUCGGGCCCGUCUUGAAACACGGACCAAGGAGUGCACAUACACUGCAAGUUGAGCAGAGGAAGUCUGUGAGGCGUAGUGAAGACGGAAAGCAGUGUGAGUGCGACCCGAUAGACUUGUGAACUAUACCUUGUUGCUGUGAAGGCUGGCGAAAGCCAGCUGGAGGCGGCAAGCCGUAUUGAUCUGCAAAUCAUUGGCGUAAGCAGGGUAUAGGGGCGAAAGACCAAUCGAACAGUCUAGUUGCUGGUUCCCUCCGAAAUGUCUAUCAGGACAGCGCGCACGCAGAGAGAAGCAAGGUAGAGCAUGGGCCGGUAUCCUUAAGGAGACGGACGAACUGCGAAUGUGCUUUUCUUCUAUGCAAGCGUAGUGGGCGAGUUCUGGUAAGCAGGACUGGCGAAGAGGAAUGAACCUGGCACUGUGCUAAGGAACCCAAUGUCUGGACAGAGACCGAAAGAGGUAGGUGAAUAAGGACGGUAGGGCGGUAGCCAUGGAAGUCGGCAUCCGGUAAGAAACGUGUUACAACGUACCUACGGAAUUCAUCUGCUCUGAAAAUUGAUGGCGCUUACCAGACAUCCGAUGCACAGUUAGCAGGUAGGAGGGCGUGUGUCUACUGGCGAAGGUACCGAGUGAUCGGUGGUGGAGGUAGAUGCAGAGCAGAUCUUGGUGGUAGUAGCGAUAAUUUGUCUUCAGCGGCAAAGACUGAGGAGGAGAAGGGUUUCUUCUCAUAAGAAGAGUGAGCCGGGUCUAAGCGAGUGUGUAGAAGCAUGAGCGAAGGAGAAACAGGUUGAUAUUCCUGUGCCUGUGCUGUCGUACGGCAACGUGUAUUAGCUUGUCGACACGAACAUCUAGACAAAGCAGAAACACCUUUUCUGUUCAAGGGGAAAAAGACCACUGAGACGGAUCAUCUGGCGACGUGGUUUUAUAUCUGUGACCAGGCCUGAGCCUGGUUUGUUGAGGAUGGUCGUCCAUGAAAAGACAACUAUAUGGCAGCACAGUCCGUACCAACCGUAUCAGGACUCCAAGGUGAAGAGCCUCUAGUGGAUGUUUUACACAUGUAAGGGAAUUCGGCAAAAUGGAUGCGUAACUUCGGGAGAAGUAUUGGUUCAAUUGUGAACUCAUUGUGACAAGGGGAAUCUGACUGUUUAGUAAAAACAUAGCUUCAUGAAGAGAGAUGAAGUGAGUUCUGCCCGGUGCUCGGUCGUGACACGGAGGAAAUGCCAGAAAGCACGGGUUAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAACGCCUCGUCAUUUAAAUGGUGACGCGCAUGAAUGGAAUGACGAGAUUCCCACUGUCCCUACAUGUAGACUAGCGAACCCAUUUCCAGGGGAACGGGCCUGGACGGCCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUGUGGCCAAGUUGUGACGAUUGAGGCGAUGUAGGAAGGUGGAGAGCGCAAGCAGAAGUGAAAGACCACUGCGCCAUGAUCAUCACGACACACUUGUUUAAGGACAAAGGCCAGAUGGGGAGUUUGGCUGGGGCGGUACGACCACAGAAUCAGAACGUGGUCGACCGAAGGUACUCACAGCGAGACGAGAACACUCGUGUAGAGCAUAAGGACUAAAGAGUGCCUGAGUGUGAGCACUACUGCUUGCAUGAGGGGAAACCCGGGCCUAGCGAUCCUACGCAUACGAGACACUUGUGGCGUGGGUGUCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCCGCCGAGCGUAGAAAGCGACGCGGCUUUUUGAUUCUUCGAUGUCGGCUCUUCCUAGCAUGGCCAUGCAGCCGUGGCGAAGUGUUGGAUUGUUCACCCACUAACAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUAUCCUACUGUCCAAACAGUUGAAGGGAGUGUGGAUUAGUACGAAAGGAAACCCACACGUGACCUCUGGUGCAGCGGGUGUGCGGAAGUGCAACUGCCAUGCUACGUCUCCUCAAGCAUAGCUGGAAGCCUCUAAGCUAGAAAUGAGUCCUGACUCUGGAAGACGGCCGGGAAGACGACCCGUAGUUAACAGCGGUGUUGUACGAUAUGAGCUUUCUAUUUGUGUAGUAGCGAGUAUUUGAGACACUGGUUGUUACCACCGUCGUUUAUU Source: (natural) Spraguea lophii 42_110 (fungus) #2: RNA chain | Mass: 38356.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) #42: RNA chain | Mass: 444812.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) |
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+60S ribosomal protein ... , 28 types, 56 molecules LA0KA0LB0KB0LC0KC0LCCKCCLD0KD0LDDKDDLE0KE0LEEKEELF0KF0LFFKFFLG0KG0LH0KH0LIIKIILJ0KJ0LJJKJJ...
-Ribosomal protein ... , 9 types, 18 molecules LAAKAALGGKGGLN0KN0LO0KO0LV0KV0LW0KW0SV0RV0SX0RX0SP0RP0
#4: Protein | Mass: 16609.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) #15: Protein | Mass: 12020.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W7C6 #26: Protein | Mass: 24200.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W7A2 #27: Protein | Mass: 22885.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XUD8 #36: Protein | Mass: 15239.987 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XLC4 #37: Protein | Mass: 15342.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XSY2 #70: Protein | Mass: 7768.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WAC1 #72: Protein | Mass: 15822.722 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) #75: Protein | Mass: 18514.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XKY9 |
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-Protein , 7 types, 14 molecules LHHKHHLI0KI0LM0KM0LMMKMMMD1MD2SFFRFFSGGRGG
#17: Protein | Mass: 14183.866 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) #18: Protein | Mass: 25142.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WBF8 #24: Protein | Mass: 13258.343 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: MYFIKPGCLIKKKFSIYTSIVISVIDNNSVVIQSYDKSDNGDVISIDREVINVSKIVPIGNIDIKNKSKKEIDGILVEENRNLKNKDDVLLMNDFERFKEQLKKEVEDMVIEEMA Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XVN9 #25: Protein | Mass: 14563.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XSQ3 #41: Protein | Mass: 17595.088 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W5K5 #54: Protein | Mass: 16937.791 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W9X5 #56: Protein | Mass: 36182.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XVG3 |
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+40S ribosomal protein ... , 28 types, 56 molecules SA0RA0SAARAASB0RB0SBBRBBSC0RC0SCCRCCSD0RD0SDDRDDSE0RE0SEEREESF0RF0SG0RG0SH0RH0SI0RI0SJ0RJ0...
-Non-polymers , 1 types, 18 molecules
#76: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Ribosome / Type: RIBOSOME / Entity ID: #1-#75 / Source: NATURAL |
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Source (natural) | Organism: Spraguea lophii 42_110 (fungus) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 20 mA, Carbon coated grid / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288.15 K / Details: blot force -1 and blot time 4 s |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | ||||||||||||||||||
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM | ||||||||||||||||||
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6000 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm | ||||||||||||||||||
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER | ||||||||||||||||||
Image recording |
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-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 14.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1344 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 20 / Num. of volumes extracted: 6505 | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: RECIPROCAL | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 14.3 Å |