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- PDB-8ovj: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : PARENTAL STRAIN -
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Basic information
Entry | Database: PDB / ID: 8ovj | ||||||
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Title | CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : PARENTAL STRAIN | ||||||
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![]() | RIBOSOME / CRYO-EM LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE | ||||||
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 / translation regulator activity / 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) / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome ...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 / translation regulator activity / 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) / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / kinase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / phosphorylation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||
![]() | 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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PDBx/mmCIF format | ![]() | 5.8 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 366 KB | Display | |
Data in CIF | ![]() | 607.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 17216MC ![]() 8a98C ![]() 8rxhC ![]() 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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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 10 types, 10 molecules 1345678S1S42
#1: RNA chain | Mass: 577046.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 321438308 |
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#2: RNA chain | Mass: 69146.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 321438308 |
#3: RNA chain | Mass: 59160.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
#4: RNA chain | Mass: 43479.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
#5: RNA chain | Mass: 23336.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 321438308 |
#6: RNA chain | Mass: 54989.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 1207899567 |
#7: RNA chain | Mass: 39450.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 321399712 |
#26: RNA chain | Mass: 710628.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
#27: RNA chain | Mass: 6451.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
#85: RNA chain | Mass: 492500.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
+Putative 60S ... , 23 types, 23 molecules AEFHIJLNOQSTUVWZacehilp
-Putative ribosomal protein ... , 7 types, 7 molecules BCSMSSXgk
#9: Protein | Mass: 47593.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q2Q6 |
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#10: Protein | Mass: 41096.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9ADW5 |
#39: Protein | Mass: 13031.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q8G4 |
#45: Protein | Mass: 6696.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q817 |
#66: Protein | Mass: 14608.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q1W6 |
#75: Protein | Mass: 16492.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QHL3 |
#79: Protein | Mass: 9479.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q8X0 |
-60S ribosomal protein ... , 10 types, 10 molecules DGPRYbdfno
#11: Protein | Mass: 21694.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P48157 |
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#14: Protein | Mass: 29824.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QIP1 |
#23: Protein | Mass: 22071.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QG98 |
#25: Protein | Mass: 20852.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q5J4 |
#67: Protein | Mass: 15469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q504 |
#70: Protein | Mass: 8001.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q178 |
#72: Protein | Mass: 11370.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AEK1 |
#74: Protein | Mass: 15458.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QC11 |
#82: Protein/peptide | Mass: 4390.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
#83: Protein | Mass: 10337.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QC01 |
-Putative 40S ribosomal protein ... , 15 types, 15 molecules KSCSDSLSNSPSRSTSUSVSWSYScSdSJ
#18: Protein | Mass: 19948.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QBJ1 |
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#30: Protein | Mass: 24511.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q4A0 |
#31: Protein | Mass: 22188.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QIM3 |
#38: Protein | Mass: 16718.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q9A5 |
#40: Protein | Mass: 18681.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q1X7 |
#42: Protein | Mass: 15969.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QC89 |
#44: Protein | Mass: 17433.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q1Y3 |
#46: Protein | Mass: 17482.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q3M1 |
#47: Protein | Mass: 20023.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
#48: Protein | Mass: 16551.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q806 |
#49: Protein | Mass: 17472.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QBV0 |
#51: Protein | Mass: 17035.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QH01 |
#55: Protein | Mass: 9819.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q140 |
#57: Protein | Mass: 9763.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q931 |
#61: Protein | Mass: 14719.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QGW3 |
-Ribosomal protein ... , 2 types, 2 molecules Mj
#20: Protein | Mass: 24497.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q6S3 |
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#78: Protein | Mass: 9862.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AEH2 |
-40S ribosomal protein ... , 15 types, 15 molecules SASBSESFSGSHSISKSOSQSXSZSaSbSe
#28: Protein | Mass: 30062.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4FX73 |
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#29: Protein | Mass: 27536.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q0Q0 |
#32: Protein | Mass: 30742.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QG31 |
#33: Protein | Mass: 28791.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QDL5 |
#34: Protein | Mass: 28370.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q9NE83 |
#35: Protein | Mass: 21336.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q868B1 |
#36: Protein | Mass: 23765.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AC32 |
#37: Protein | Mass: 24984.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P25204 |
#41: Protein | Mass: 15623.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q8H1 |
#43: Protein | Mass: 15627.837 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QG97 |
#50: Protein | Mass: 18158.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AEE8 |
#52: Protein | Mass: 15808.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q1D2 |
#54: Protein | Mass: 13071.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q9X4 |
#56: Protein | Mass: 12794.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q8L6 |
#58: Protein | Mass: 7394.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q7P0 |
-Protein , 3 types, 3 molecules SgShm
#59: Protein | Mass: 34441.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q7Y7 |
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#60: Protein | Mass: 25229.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q5K7 |
#81: Protein | Mass: 14711.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P69201 |
-Non-polymers , 5 types, 416 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#86: Chemical | ChemComp-MG / #87: Chemical | ChemComp-K / #88: Chemical | ChemComp-NA / #89: Chemical | ChemComp-ZN / #90: Water | ChemComp-HOH / | |
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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: single particle reconstruction |
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Sample preparation
Component | Name: 80S RIBOSOME FROM LEISHMANIA MAJOR / Type: RIBOSOME / Entity ID: #1-#85 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.6 |
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 / Nominal defocus max: 1300 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 0.83 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: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212912 / Symmetry type: POINT | ||||||||||||||||||||||||
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