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- PDB-6zqf: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zqf | ||||||
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Title | Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-B (Poly-Ala) | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cheng, J. / Lau, B. / Venuta, G.L. / Berninghausen, O. / Hurt, E. / Beckmann, R. | ||||||
![]() | ![]() Title: 90 pre-ribosome transformation into the primordial 40 subunit. Authors: Jingdong Cheng / Benjamin Lau / Giuseppe La Venuta / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann / ![]() Abstract: Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this ...Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90 pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A, thereby separating the 5'-external transcribed spacer (ETS) from 18 ribosomal RNA. Next, the 5'-ETS and 90 assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40 emerges, still retaining some 90 factors including Dhr1, now ready to unwind the final small nucleolar U3-18 RNA hybrid. Our data shed light on the elusive 90 to pre-40 transition and clarify the principles of assembly and remodeling of large ribonucleoproteins. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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-Validation report
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-Related structure data
Related structure data | ![]() 11362MC ![]() 6zqaC ![]() 6zqbC ![]() 6zqcC ![]() 6zqdC ![]() 6zqeC ![]() 6zqgC 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
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Components
-Protein , 11 types, 12 molecules UAUCCLCMCNJDJFJGJHJLJJDF
#1: Protein | Mass: 104097.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P25635 | ||||||||
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#3: Protein | Mass: 70364.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12136 | ||||||||
#12: Protein | ![]() Mass: 135792.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q08965 | ||||||||
#13: Protein | Mass: 40220.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q08096 | ||||||||
#14: Protein | Mass: 34526.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P25368 | ||||||||
#15: Protein | Mass: 145171.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q04217, ![]() | ||||||||
#16: Protein | ![]() Mass: 27936.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c References: UniProt: Q06287, ![]() #17: Protein | | Mass: 55207.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38333 #18: Protein | | Mass: 36003.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c References: UniProt: P41819, ![]() #19: Protein | | Mass: 30380.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q99216 #20: Protein | | Mass: 25072.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P26783 |
-Nucleolar complex protein ... , 2 types, 2 molecules UBUS
#2: Protein | Mass: 94463.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q99207 |
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#6: Protein | Mass: 63707.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q06512 |
-U3 small nucleolar RNA-associated protein ... , 5 types, 5 molecules ULUMUUUVCK
#4: Protein | Mass: 106481.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12220 |
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#5: Protein | Mass: 91132.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q05946 |
#7: Protein | Mass: 104927.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q06078 |
#8: Protein | Mass: 140660.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P53254 |
#11: Protein | Mass: 67042.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P47083 |
-U3 small nucleolar ribonucleoprotein protein ... , 2 types, 2 molecules CICJ
#9: Protein | Mass: 21928.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P32899 |
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#10: Protein | Mass: 33536.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P53941 |
-40S ribosomal protein ... , 18 types, 18 molecules DQDSDTDcDADEDGDHDIDJDLDNDODZDWDXDYDb
#21: Protein | ![]() Mass: 15877.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CX51 |
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#22: Protein | ![]() Mass: 17071.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CX55 |
#23: Protein | ![]() Mass: 15942.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P07280 |
#24: Protein | ![]() Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q3E7X9 |
#27: Protein | ![]() Mass: 28798.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P33442 |
#28: Protein | ![]() Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CX35 |
#29: Protein | ![]() Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CX37 |
#30: Protein | ![]() Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P26786 |
#31: Protein | ![]() Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CX39 |
#32: Protein | ![]() Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: O13516 |
#33: Protein | ![]() Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CX47 |
#34: Protein | ![]() Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P05756 |
#35: Protein | ![]() Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P06367 |
#36: Protein | ![]() Mass: 12067.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q3E792 |
#37: Protein | ![]() Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0C0W1 |
#38: Protein | ![]() Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CX29 |
#39: Protein | ![]() Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CX31 |
#40: Protein | ![]() Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P35997 |
-RNA chain , 3 types, 3 molecules D2D3D4
#25: RNA chain | Mass: 6441.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#26: RNA chain | ![]() Mass: 566062.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#41: RNA chain | Mass: 11187.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-Non-polymers , 1 types, 1 molecules ![](data/chem/img/ZN.gif)
#42: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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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
Component | Name: 90S pre-ribbosome state Dis-B / Type: RIBOSOME / Entity ID: #1-#41 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Specimen support | Grid material: COPPER / Grid type: Quantifoil |
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: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction![]() | Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16654 / Symmetry type: POINT |