+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10624 | |||||||||
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Title | Drosophila melanogaster Ovary 80S ribosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Specialised ribosome / Drosophila melanogaster / Ovary / RIBOSOME | |||||||||
Function / homology | Function and homology information 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 / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol ...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 / 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 / Protein methylation / ER Quality Control Compartment (ERQC) / Iron uptake and transport / RAS processing / Pexophagy / Regulation of BACH1 activity / Regulation of pyruvate metabolism / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Translesion synthesis by POLK / Translesion synthesis by POLI / Ovarian tumor domain proteases / Formation of Incision Complex in GG-NER / Formation of TC-NER Pre-Incision Complex / Regulation of expression of SLITs and ROBOs / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Translesion Synthesis by POLH / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / APC-Cdc20 mediated degradation of Nek2A / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / Ubiquitination and degradation of phosphorylated ARM / Separation of Sister Chromatids / Degradation of AXIN / Degradation of DVL / Regulation of TNFR1 signaling / Dectin-1 mediated noncanonical NF-kB signaling / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / NIK-->noncanonical NF-kB signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / Regulation of RUNX3 expression and activity / Peroxisomal protein import / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex / Downregulation of ERBB2:ERBB3 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / Nuclear CI is degraded / ABC-family proteins mediated transport / TAK1-dependent IKK and NF-kappa-B activation / activated TAK1 mediates p38 MAPK activation / PINK1-PRKN Mediated Mitophagy / Hedgehog ligand biogenesis / Josephin domain DUBs / Dual Incision in GG-NER / Dual incision in TC-NER / Downregulation of ERBB2 signaling / VLDLR internalisation and degradation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK1 recruits IKK complex / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / KEAP1-NFE2L2 pathway / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Ubiquitination and proteolysis of phosphorylated CI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Spry regulation of FGF signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Interleukin-1 signaling / Regulation of signaling by CBL / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / pupariation / Downregulation of ERBB4 signaling / Degradation of PER / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Protein hydroxylation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Deactivation of the beta-catenin transactivating complex / Regulation of necroptotic cell death Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Hopes T / Agapiou M | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nucleic Acids Res / Year: 2022 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10624.map.gz | 141.6 MB | EMDB map data format | |
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Header (meta data) | emd-10624-v30.xml emd-10624.xml | 93.7 KB 93.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10624_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_10624.png | 172.4 KB | ||
Filedesc metadata | emd-10624.cif.gz | 18.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10624 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10624 | HTTPS FTP |
-Validation report
Summary document | emd_10624_validation.pdf.gz | 516.7 KB | Display | EMDB validaton report |
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Full document | emd_10624_full_validation.pdf.gz | 516.3 KB | Display | |
Data in XML | emd_10624_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_10624_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10624 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10624 | HTTPS FTP |
-Related structure data
Related structure data | 6xu8MC 6xu6C 6xu7C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10624.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: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Drosophila melanogaster ovary 80S ribosome
+Supramolecule #1: Drosophila melanogaster ovary 80S ribosome
+Macromolecule #1: 60S ribosomal protein L13a
+Macromolecule #2: 60S ribosomal protein L13
+Macromolecule #3: 60S ribosomal protein L23
+Macromolecule #4: 60S ribosomal protein L14
+Macromolecule #5: 60S ribosomal protein L27a
+Macromolecule #6: 60S ribosomal protein L15
+Macromolecule #7: 60S ribosomal protein L10
+Macromolecule #8: 60S ribosomal protein L5
+Macromolecule #9: 60S ribosomal protein L18
+Macromolecule #10: 60S ribosomal protein L19
+Macromolecule #11: 60S ribosomal protein L8
+Macromolecule #12: 60S ribosomal protein L18a
+Macromolecule #13: RE62581p
+Macromolecule #14: 60S ribosomal protein L17
+Macromolecule #15: IP17216p
+Macromolecule #16: GEO07453p1
+Macromolecule #17: 60S ribosomal protein L27
+Macromolecule #18: 60S ribosomal protein L28
+Macromolecule #19: FI02809p
+Macromolecule #20: 60S ribosomal protein L29
+Macromolecule #21: 60S ribosomal protein L3
+Macromolecule #22: 60S ribosomal protein L7
+Macromolecule #23: RE25263p
+Macromolecule #24: 60S ribosomal protein L32
+Macromolecule #25: GEO07455p1
+Macromolecule #26: 60S ribosomal protein L36
+Macromolecule #27: 60S ribosomal protein L38
+Macromolecule #28: 60S ribosomal protein L39
+Macromolecule #29: 60S ribosomal protein L4
+Macromolecule #30: Ubiquitin-60S ribosomal protein L40
+Macromolecule #31: 60S ribosomal protein L41
+Macromolecule #32: 60S ribosomal protein L37a
+Macromolecule #33: TA01007p
+Macromolecule #34: 60S ribosomal protein L11
+Macromolecule #35: 60S ribosomal protein L9
+Macromolecule #36: Ribosomal protein L6, isoform A
+Macromolecule #37: 60S ribosomal protein L7a
+Macromolecule #41: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #42: 40S ribosomal protein S20
+Macromolecule #43: 40S ribosomal protein S14a
+Macromolecule #44: 40S ribosomal protein S23
+Macromolecule #45: 40S ribosomal protein S12
+Macromolecule #46: 40S ribosomal protein S29
+Macromolecule #47: 40S ribosomal protein S13
+Macromolecule #48: 40S ribosomal protein S11
+Macromolecule #49: 40S ribosomal protein S17
+Macromolecule #50: GEO07301p1
+Macromolecule #51: 40S ribosomal protein S3a
+Macromolecule #52: 40S ribosomal protein SA
+Macromolecule #53: 40S ribosomal protein S21
+Macromolecule #54: 40S ribosomal protein S24
+Macromolecule #55: 40S ribosomal protein S25
+Macromolecule #56: 40S ribosomal protein S26
+Macromolecule #57: 40S ribosomal protein S27
+Macromolecule #58: 40S ribosomal protein S3
+Macromolecule #59: 40S ribosomal protein S30
+Macromolecule #60: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #61: 40S ribosomal protein S9
+Macromolecule #62: 40S ribosomal protein S4
+Macromolecule #63: 40S ribosomal protein S2
+Macromolecule #64: 40S ribosomal protein S6
+Macromolecule #65: 40S ribosomal protein S7
+Macromolecule #66: 40S ribosomal protein S8
+Macromolecule #67: 40S ribosomal protein S16
+Macromolecule #68: 60S ribosomal protein L10a-2
+Macromolecule #71: 40S ribosomal protein S15Aa
+Macromolecule #72: 40S ribosomal protein S19a
+Macromolecule #73: 40S ribosomal protein S10b
+Macromolecule #74: 40S ribosomal protein S5b
+Macromolecule #75: 40S ribosomal protein S28
+Macromolecule #76: 60S ribosomal protein L22
+Macromolecule #77: Probable 60S ribosomal protein L37-A
+Macromolecule #78: 60S ribosomal protein L24
+Macromolecule #79: 60S ribosomal protein L34
+Macromolecule #80: 60S ribosomal protein L31
+Macromolecule #81: 40S ribosomal protein S18
+Macromolecule #38: 2S ribosomal RNA
+Macromolecule #39: 5S ribosomal RNA
+Macromolecule #40: 5.8S ribosomal RNA
+Macromolecule #69: 28S ribosomal RNA
+Macromolecule #70: 18S ribosomal RNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-6xu8: |