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- PDB-6lqt: Cryo-EM structure of 90S small subunit preribosomes in transition... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6lqt | |||||||||
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Title | Cryo-EM structure of 90S small subunit preribosomes in transition states (State E) | |||||||||
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Function / homology | ![]() Noc4p-Nop14p complex / box H/ACA snoRNA binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Du, Y. / Ye, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of 90 small ribosomal subunit precursors in transition states. Authors: Yifei Du / Weidong An / Xing Zhu / Qi Sun / Jia Qi / Keqiong Ye / ![]() Abstract: The 90 preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 ribosome. Here, we gained insight into this transition by ...The 90 preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 ribosome. Here, we gained insight into this transition by determining cryo-electron microscopy structures of intermediates in the path from the 90 to the pre-40 The full transition is blocked by deletion of RNA helicase Dhr1. A series of structural snapshots revealed that the excised 5' external transcribed spacer (5' ETS) is degraded within 90, driving stepwise disassembly of assembly factors and ribosome maturation. The nuclear exosome, an RNA degradation machine, docks on the 90 through helicase Mtr4 and is primed to digest the 3' end of the 5' ETS. The structures resolved between 3.2- and 8.6-angstrom resolution reveal key intermediates and the critical role of 5' ETS degradation in 90 progression. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 4 MB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 0953MC ![]() 0949C ![]() 0950C ![]() 0951C ![]() 0952C ![]() 0954C ![]() 0955C ![]() 6lqpC ![]() 6lqqC ![]() 6lqrC ![]() 6lqsC ![]() 6lquC ![]() 6lqvC 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
-RNA chain , 3 types, 3 molecules 3A5ASA
#1: RNA chain | Mass: 106503.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#2: RNA chain | Mass: 225543.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#3: RNA chain | Mass: 582710.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-40S ribosomal protein ... , 16 types, 16 molecules SCSFSGSHSISJSKSMSOSPSRSXSYSZScSd
#4: 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 |
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#5: 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 |
#6: 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 |
#7: 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 |
#8: 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 |
#9: 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 |
#10: 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 |
#11: 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 |
#12: 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 |
#13: 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 |
#14: 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 |
#15: Protein | ![]() Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q3E7Y3 |
#16: 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 |
#17: 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 |
#18: 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 |
#19: 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 |
-Protein , 13 types, 15 molecules 3B3C3G3HAGB15H5IRDRHRJRKRNRTX1
#20: Protein | Mass: 34525.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c References: UniProt: P15646, ![]() #24: Protein | Mass: 13582.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P39990 #30: Protein | | Mass: 101341.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q02931 #31: 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 #42: 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 #43: Protein | | Mass: 56888.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P33750 #46: Protein | | Mass: 193411.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q05022 #49: Protein | | ![]() Mass: 27936.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c References: UniProt: Q06287, ![]() #50: 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 #51: 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 #52: 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 #55: Protein | | ![]() Mass: 36356.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #56: Protein | | Mass: 29549.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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-Nucleolar protein ... , 2 types, 2 molecules 3D3E
#21: Protein | ![]() Mass: 56961.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12460 |
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#22: Protein | ![]() Mass: 57060.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12499 |
-Ribosomal RNA-processing protein ... , 2 types, 2 molecules 3FRF
#23: Protein | Mass: 64999.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q06506 |
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#48: 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 |
-U3 small nucleolar RNA-associated protein ... , 16 types, 16 molecules A4A5A9AEAFB2B3B8BEB65C5D5ERERPRQ
#25: Protein | Mass: 87909.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q06679 |
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#26: Protein | Mass: 72079.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q04177 |
#27: Protein | Mass: 65347.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38882 |
#28: Protein | Mass: 200298.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P42945 |
#29: Protein | Mass: 57765.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q04305 |
#32: 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 |
#33: 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 |
#34: Protein | Mass: 66494.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40362 |
#35: 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 |
#36: Protein | Mass: 52495.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q02354 |
#37: Protein | Mass: 62418.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40055 |
#38: Protein | Mass: 29806.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P34247 |
#39: 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 |
#47: 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 |
#53: Protein | Mass: 287915.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P35194 |
#54: Protein | Mass: 103189.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q04500 |
-U3 small nucleolar ribonucleoprotein protein ... , 2 types, 2 molecules 5F5G
#40: 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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#41: 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 |
-RRNA-processing protein ... , 2 types, 2 molecules 5J5K
#44: Protein | Mass: 25689.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12035 |
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#45: Protein | Mass: 21650.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q05498 |
-Non-polymers , 3 types, 4 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
#57: Chemical | #58: Chemical | ChemComp-GTP / | ![]() #59: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | N |
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Sequence details | The authors don't know the sequence of Chain X1.The residue numbers in the coordinates may be meaningless. |
-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-ribosome (Dhr1-depleted, state E) / Type: COMPLEX / Entity ID: #1-#56 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 5 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() ![]() ![]() Strain: ATCC 204508 / S288c | |||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 10 / Num. of real images: 18028 |
Image scans | Movie frames/image: 32 / Used frames/image: 1-32 |
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Processing
EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 382298 | ||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14475 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6LQS Accession code: 6LQS / Source name: PDB / Type: experimental model |