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- PDB-8rxh: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-sit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rxh | ||||||
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Title | CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA : PARENTAL STRAIN | ||||||
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Function / homology | ![]() ciliary transition zone / nuclear lumen / ciliary plasm / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...ciliary transition zone / nuclear lumen / ciliary plasm / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rajan, K.S. / Yonath, A. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Structural and mechanistic insights into the function of Leishmania ribosome lacking a single pseudouridine modification. Authors: K Shanmugha Rajan / Saurav Aryal / Disha-Gajanan Hiregange / Anat Bashan / Hava Madmoni / Mika Olami / Tirza Doniger / Smadar Cohen-Chalamish / Pascal Pescher / Masato Taoka / Yuko Nobe / ...Authors: K Shanmugha Rajan / Saurav Aryal / Disha-Gajanan Hiregange / Anat Bashan / Hava Madmoni / Mika Olami / Tirza Doniger / Smadar Cohen-Chalamish / Pascal Pescher / Masato Taoka / Yuko Nobe / Aliza Fedorenko / Tanaya Bose / Ella Zimermann / Eric Prina / Noa Aharon-Hefetz / Yitzhak Pilpel / Toshiaki Isobe / Ron Unger / Gerald F Späth / Ada Yonath / Shulamit Michaeli / ![]() ![]() ![]() Abstract: Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the ...Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the parasite life cycle. Alterations in the level of a specific Ψ in helix 69 (H69) affected ribosome function. To decipher the molecular mechanism of this phenotype, we determine the structure of ribosomes lacking the single Ψ and its parental strain at ∼2.4-3 Å resolution using cryo-EM. Our findings demonstrate the significance of a single Ψ on H69 to its structure and the importance for its interactions with helix 44 and specific tRNAs. Our study suggests that rRNA modification affects translation of mRNAs carrying codon bias due to selective accommodation of tRNAs by the ribosome. Based on the high-resolution structures, we propose a mechanism explaining how the ribosome selects specific tRNAs. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 5.3 MB | Display | ![]() |
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PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 19576MC ![]() 8a98C ![]() 8ovjC ![]() 8rxxC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
+RNA chain , 13 types, 13 molecules L1L2L3L4L5L6L7L8S1S2S3S4S5
+Putative 60S ... , 23 types, 23 molecules LALELFLHLILJLLLNLOLQLSLTLULVLWLZLaLcLeLhLiLlLp
+Putative ribosomal protein ... , 7 types, 7 molecules LBLCLXLgLkSMSS
+60S ribosomal protein ... , 10 types, 10 molecules LDLGLPLRLYLbLdLfLnLo
+Putative 40S ribosomal protein ... , 14 types, 14 molecules LKSCSDSJSLSNSPSRSTSVSWSYScSd
+Ribosomal protein ... , 3 types, 3 molecules LMLjSU
+Ubiquitin-60S ribosomal protein ... , 2 types, 2 molecules LmSf
+40S ribosomal protein ... , 15 types, 15 molecules SASBSESFSGSHSISKSOSQSXSZSaSbSe
+Protein , 2 types, 2 molecules SgSh
+Non-polymers , 6 types, 933 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
+Details
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA Type: RIBOSOME / Entity ID: #1-#7, #9-#50, #52-#89 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() Details: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 |
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: 0.93403907986206 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20.1_4487 / Category: model refinement |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction![]() | Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 419524 / Symmetry type: POINT |