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Open data
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Basic information
Entry | Database: PDB / ID: 6xu6 | |||||||||
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Title | Drosophila melanogaster Testis 80S ribosome | |||||||||
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![]() | RIBOSOME / Specialised ribosome / Drosophila melanogaster / Testis | |||||||||
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 / Protein methylation / ER Quality Control Compartment (ERQC) / Iron uptake and transport / RAS processing / Pexophagy / Regulation of BACH1 activity / 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 / 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 / PINK1-PRKN Mediated Mitophagy / Dectin-1 mediated noncanonical NF-kB signaling / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / NIK-->noncanonical NF-kB signaling / Josephin domain DUBs / 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 / Regulation of expression of SLITs and ROBOs / Peroxisomal protein import / KEAP1-NFE2L2 pathway / 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 / 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 / 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 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 / Hedgehog ligand biogenesis / Regulation of necroptotic cell death / EGFR downregulation / Degradation of PER Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Hopes, T. / Agapiou, M. / Norris, K. / McCarthy, C.G.P. / OConnell, M.J. / Fontana, J. / Aspden, J.L. | |||||||||
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 | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 4.9 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 502.3 KB | Display | |
Data in CIF | ![]() | 814.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 10622MC ![]() 6xu7C ![]() 6xu8C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
+40S ribosomal protein ... , 30 types, 30 molecules AAABACAUAXAMAdANALARAVAYAZAaAbADAeAJAEAGAHAIAQAKATAFAOAcAWAS
+60S ribosomal protein ... , 31 types, 31 molecules CACBCCCaCNCICDCQCRCSCPCZCrCbCeCiCkClCnCpCJCHCGCzCOCLCVCMCWCFCd
-Protein , 14 types, 14 molecules AgAPAfCTCXCYChCcCfCmCoDACgCj
#7: Protein | Mass: 35661.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#15: Protein | Mass: 14504.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: Protein | Mass: 9421.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#32: Protein | Mass: 18388.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#34: Protein | Mass: 13981.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#35: Protein | Mass: 15337.095 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#38: Protein | Mass: 14491.677 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#40: Protein | Mass: 11035.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#42: Protein | Mass: 17701.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#46: Protein | Mass: 6200.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#49: Protein | Mass: 12540.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#69: Protein | Mass: 41409.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#77: Protein | Mass: 12095.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#79: Protein | Mass: 9978.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Ribosomal protein ... , 2 types, 2 molecules CECU
#52: Protein | Mass: 26179.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#78: Protein | Mass: 11525.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain , 5 types, 5 molecules A9A7A8B2A5
#54: RNA chain | Mass: 9665.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#55: RNA chain | Mass: 38627.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#56: RNA chain | Mass: 39616.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#58: RNA chain | Mass: 641830.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#59: RNA chain | Mass: 1278930.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Drosophila melanogaster testis 80S ribosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46878 / Symmetry type: POINT |
Atomic model building | Protocol: FLEXIBLE FIT |
Atomic model building | PDB-ID: 4V6W |