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- PDB-6ft6: Structure of the Nop53 pre-60S particle bound to the exosome nucl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ft6 | ||||||
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Title | Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors | ||||||
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Function / homology | ![]() nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schuller, J.M. / Falk, S. / Conti, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the nuclear exosome captured on a maturing preribosome. Authors: Jan Michael Schuller / Sebastian Falk / Lisa Fromm / Ed Hurt / Elena Conti / ![]() Abstract: The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex ...The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60) during 7-to-5.8 rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 particle, which harbors the 5.8 rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 rRNA, captures the 3' extension of the 5.8 rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 substrate to process rRNA during ribosome maturation. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 3.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
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 | ![]() 4302MC ![]() 4301C ![]() 6fszC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 3 types, 3 molecules 213
#1: RNA chain | ![]() Mass: 51999.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: ![]() |
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#50: RNA chain | ![]() Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: ![]() |
#51: RNA chain | ![]() Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: ![]() |
+60S ribosomal protein ... , 35 types, 35 molecules ABCDEFGHJLMNOPQRSTUVXYZacdefgh...
-Protein , 9 types, 9 molecules Inswyz45MM
#10: Protein | Mass: 18546.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: Q08004 |
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#40: Protein | Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P53261 |
#43: Protein | Mass: 57798.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P40010 |
#46: Protein | Mass: 23001.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: Q08746 |
#48: Protein | Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: Q12522 |
#49: Protein | Mass: 12435.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P38202 |
#52: Protein | Mass: 65290.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: Q03862, ![]() |
#53: Protein | Mass: 14460.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P53188 |
#56: Protein | Mass: 115230.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: MTR4, DOB1, YJL050W, J1158 / Production host: ![]() ![]() ![]() ![]() |
-Ribosome assembly ... , 2 types, 2 molecules Wx
#23: Protein | Mass: 27098.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P33201 |
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#47: Protein | Mass: 57106.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P25382 |
-Nucleolar GTP-binding protein ... , 2 types, 2 molecules bm
#28: Protein | Mass: 74531.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: Q02892 |
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#39: Protein | Mass: 55585.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P53742 |
-Ribosome biogenesis protein ... , 3 types, 3 molecules ruv
#42: Protein | ![]() Mass: 29786.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P40078 |
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#44: Protein | ![]() Mass: 24027.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: Q07915 |
#45: Protein | ![]() Mass: 39665.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P36160 |
-Exosome complex ... , 2 types, 2 molecules KKLL
#54: Protein | Mass: 84160.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: RRP6, UNC733, YOR001W / Production host: ![]() ![]() ![]() References: UniProt: Q12149, ![]() |
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#55: Protein | ![]() Mass: 21086.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: LRP1, RRP47, YC1D, YHR081W / Production host: ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules NN
#57: Protein/peptide | ![]() Mass: 954.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() ![]() |
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-Non-polymers , 3 types, 8 molecules ![](data/chem/img/ZN.gif)
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![](data/chem/img/MG.gif)
#58: Chemical | ChemComp-ZN / #59: Chemical | ![]() #60: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||
Vitrification![]() | Cryogen name: ETHANE-PROPANE |
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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: 38.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.13rc2_2986: / Classification: refinement |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction![]() | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22439 / Symmetry type: POINT |