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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10622 | |||||||||
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Title | Drosophila melanogaster Testis 80S ribosome | |||||||||
![]() | Drosophila melanogaster testis 80S ribosome | |||||||||
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Function / homology | ![]() APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / Activation of the IkappaB kinase complex, KEY:IRD5 dimer:KEY / NF-kB is activated and signals survival / Downregulation of TGF-beta receptor signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Regulation of innate immune responses to cytosolic DNA / Regulation of TNFR1 signaling / Gap-filling DNA repair synthesis and ligation in TC-NER ...APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / Activation of the IkappaB kinase complex, KEY:IRD5 dimer:KEY / NF-kB is activated and signals survival / Downregulation of TGF-beta receptor signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Regulation of innate immune responses to cytosolic DNA / Regulation of TNFR1 signaling / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / Regulation of TP53 Degradation / Cyclin D associated events in G1 / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / GTP hydrolysis and joining of the 60S ribosomal subunit / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Hopes T / Agapiou M / Norris K / McCarthy CGP / OConnell MJ / Fontana J / Aspden JL | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching. Authors: Tayah Hopes / Karl Norris / Michaela Agapiou / Charley G P McCarthy / Philip A Lewis / Mary J O'Connell / Juan Fontana / Julie L Aspden / ![]() Abstract: Ribosomes have long been thought of as homogeneous macromolecular machines, but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have ...Ribosomes have long been thought of as homogeneous macromolecular machines, but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have characterised ribosomal protein heterogeneity across 4 tissues of Drosophila melanogaster. We find that testes and ovaries contain the most heterogeneous ribosome populations, which occurs through a combination of paralog-enrichment and paralog-switching. We have solved structures of ribosomes purified from in vivo tissues by cryo-EM, revealing differences in precise ribosomal arrangement for testis and ovary 80S ribosomes. Differences in the amino acid composition of paralog pairs and their localisation on the ribosome exterior indicate paralog-switching could alter the ribosome surface, enabling different proteins to regulate translation. One testis-specific paralog-switching pair is also found in humans, suggesting this is a conserved site of ribosome heterogeneity. Overall, this work allows us to propose that mRNA translation might be regulated in the gonads through ribosome heterogeneity, providing a potential means of ribosome specialisation. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 141.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 87.7 KB 87.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 151.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xu6MC ![]() 6xu7C ![]() 6xu8C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Drosophila melanogaster testis 80S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Drosophila melanogaster testis 80S ribosome
+Supramolecule #1: Drosophila melanogaster testis 80S ribosome
+Macromolecule #1: 40S ribosomal protein SA
+Macromolecule #2: 60S ribosomal protein L8
+Macromolecule #3: 40S ribosomal protein S3a
+Macromolecule #4: 60S ribosomal protein L3
+Macromolecule #5: 40S ribosomal protein S2
+Macromolecule #6: 60S ribosomal protein L4
+Macromolecule #7: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #8: 40S ribosomal protein S20
+Macromolecule #9: 40S ribosomal protein S23
+Macromolecule #10: 40S ribosomal protein S12
+Macromolecule #11: 40S ribosomal protein S29
+Macromolecule #12: 40S ribosomal protein S13
+Macromolecule #13: 40S ribosomal protein S11
+Macromolecule #14: 40S ribosomal protein S17
+Macromolecule #15: GEO07301p1
+Macromolecule #16: 40S ribosomal protein S21
+Macromolecule #17: 40S ribosomal protein S24
+Macromolecule #18: 40S ribosomal protein S25
+Macromolecule #19: 40S ribosomal protein S26
+Macromolecule #20: 40S ribosomal protein S27
+Macromolecule #21: 40S ribosomal protein S3
+Macromolecule #22: 40S ribosomal protein S30
+Macromolecule #23: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #24: 40S ribosomal protein S9
+Macromolecule #25: 60S ribosomal protein L27a
+Macromolecule #26: 60S ribosomal protein L15
+Macromolecule #27: 60S ribosomal protein L10
+Macromolecule #28: 60S ribosomal protein L5
+Macromolecule #29: 60S ribosomal protein L18
+Macromolecule #30: 60S ribosomal protein L19
+Macromolecule #31: 60S ribosomal protein L18a
+Macromolecule #32: RE62581p
+Macromolecule #33: 60S ribosomal protein L17
+Macromolecule #34: IP17216p
+Macromolecule #35: GEO07453p1
+Macromolecule #36: 60S ribosomal protein L27
+Macromolecule #37: 60S ribosomal protein L28
+Macromolecule #38: FI02809p
+Macromolecule #39: 60S ribosomal protein L29
+Macromolecule #40: RE25263p
+Macromolecule #41: 60S ribosomal protein L32
+Macromolecule #42: GEO07455p1
+Macromolecule #43: 60S ribosomal protein L36
+Macromolecule #44: 60S ribosomal protein L38
+Macromolecule #45: 60S ribosomal protein L39
+Macromolecule #46: Ubiquitin-60S ribosomal protein L40
+Macromolecule #47: 60S ribosomal protein L41
+Macromolecule #48: 60S ribosomal protein L37a
+Macromolecule #49: TA01007p
+Macromolecule #50: 60S ribosomal protein L11
+Macromolecule #51: 60S ribosomal protein L9
+Macromolecule #52: Ribosomal protein L6, isoform A
+Macromolecule #53: 60S ribosomal protein L7a
+Macromolecule #57: 60S ribosomal protein L10a-2
+Macromolecule #60: 40S ribosomal protein S4
+Macromolecule #61: 40S ribosomal protein S6
+Macromolecule #62: 40S ribosomal protein S7
+Macromolecule #63: 40S ribosomal protein S8
+Macromolecule #64: 40S ribosomal protein S16
+Macromolecule #65: 60S ribosomal protein L13a
+Macromolecule #66: 60S ribosomal protein L13
+Macromolecule #67: 60S ribosomal protein L23
+Macromolecule #68: 60S ribosomal protein L14
+Macromolecule #69: LP04564p
+Macromolecule #70: 40S ribosomal protein S10b
+Macromolecule #71: 40S ribosomal protein S19a
+Macromolecule #72: 40S ribosomal protein S5a
+Macromolecule #73: 40S ribosomal protein S14a
+Macromolecule #74: 40S ribosomal protein S28
+Macromolecule #75: 40S ribosomal protein S15Aa
+Macromolecule #76: 60S ribosomal protein L24
+Macromolecule #77: RH48056p
+Macromolecule #78: Ribosomal protein L22-like protein
+Macromolecule #79: Probable 60S ribosomal protein L37-B
+Macromolecule #80: 60S ribosomal protein L7
+Macromolecule #81: 60S ribosomal protein L31
+Macromolecule #82: 40S ribosomal protein S18
+Macromolecule #54: 2S ribosomal RNA
+Macromolecule #55: 5S ribosomal RNA
+Macromolecule #56: 5.8S ribosomal RNA
+Macromolecule #58: 18S ribosomal RNA
+Macromolecule #59: 28S ribosomal RNA
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 80.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |