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- EMDB-11357: 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: EMDB / ID: EMD-11357 | |||||||||
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Title | Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state A (Poly-Ala) | |||||||||
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![]() | 90S pre-ribbosome state A
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Function / homology | ![]() Noc4p-Nop14p complex / CURI complex / t-UTP complex / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / sno(s)RNA processing / RNA fragment catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Cheng J / Lau B / Venuta GL / 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. | |||||||||
Validation Report | ![]() ![]() ![]() ![]() | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
FSC (resolution estimation) |
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Header (meta data in XML format) |
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Images |
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Archive directory |
-Related structure data
Related structure data | ![]() 6zqaCM ![]() 6zqbC ![]() 6zqcC ![]() 6zqdC ![]() 6zqeC ![]() 6zqfC ![]() 6zqgC C: citing same article ( M: atomic model generated by this map |
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Similar-shape strucutres |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire 90S pre-ribbosome state A
+Component #1: protein, 90S pre-ribbosome state A
+Component #2: protein, Periodic tryptophan protein 2
+Component #3: protein, Nucleolar complex protein 14
+Component #4: protein, Something about silencing protein 10
+Component #5: protein, U3 small nucleolar RNA-associated protein 4
+Component #6: protein, U3 small nucleolar RNA-associated protein 5
+Component #7: protein, U3 small nucleolar RNA-associated protein 6
+Component #8: protein, U3 small nucleolar RNA-associated protein 7
+Component #9: protein, U3 small nucleolar RNA-associated protein 8
+Component #10: protein, U3 small nucleolar RNA-associated protein 9
+Component #11: protein, U3 small nucleolar RNA-associated protein 10
+Component #12: protein, U3 small nucleolar RNA-associated protein 11
+Component #13: protein, U3 small nucleolar RNA-associated protein 12
+Component #14: protein, U3 small nucleolar RNA-associated protein 13
+Component #15: protein, U3 small nucleolar RNA-associated protein 14
+Component #16: protein, U3 small nucleolar RNA-associated protein 15
+Component #17: protein, Bud site selection protein 21
+Component #18: protein, NET1-associated nuclear protein 1
+Component #19: protein, U3 small nucleolar RNA-associated protein 18
+Component #20: protein, Nucleolar complex protein 4
+Component #21: protein, U3 small nucleolar RNA-associated protein 21
+Component #22: protein, U3 small nucleolar RNA-associated protein 22
+Component #23: protein, rRNA-processing protein FCF1
+Component #24: protein, Ribosome biogenesis protein UTP30
+Component #25: protein, rRNA 2'-O-methyltransferase fibrillarin
+Component #26: protein, Nucleolar protein 56
+Component #27: protein, Nucleolar protein 58
+Component #28: protein, 13 kDa ribonucleoprotein-associated protein
+Component #29: protein, Ribosomal RNA-processing protein 9
+Component #30: protein, U3 small nucleolar ribonucleoprotein protein IMP3
+Component #31: protein, U3 small nucleolar ribonucleoprotein protein IMP4
+Component #32: protein, U3 small nucleolar RNA-associated protein MPP10
+Component #33: protein, Ribosome biogenesis protein BMS1
+Component #34: protein, RNA 3'-terminal phosphate cyclase-like protein
+Component #35: protein, Ribosomal RNA-processing protein 7
+Component #36: protein, Ribosomal RNA small subunit methyltransferase NEP1
+Component #37: protein, Essential nuclear protein 1
+Component #38: protein, Pre-rRNA-processing protein PNO1
+Component #39: protein, rRNA-processing protein FCF2
+Component #40: protein, Protein FAF1
+Component #41: protein, KRR1 small subunit processome component
+Component #42: protein, Protein SOF1
+Component #43: protein, Regulator of rDNA transcription protein 14
+Component #44: protein, 40S ribosomal protein S1-A
+Component #45: protein, Rps5p
+Component #46: protein, 40S ribosomal protein S7-A
+Component #47: protein, 40S ribosomal protein S9-A
+Component #48: protein, 40S ribosomal protein S13
+Component #49: protein, 40S ribosomal protein S14-A
+Component #50: protein, 40S ribosomal protein S16-A
+Component #51: protein, 40S ribosomal protein S18-A
+Component #52: protein, 40S ribosomal protein S22-A
+Component #53: protein, 40S ribosomal protein S23-A
+Component #54: protein, 40S ribosomal protein S27-A
+Component #55: protein, 40S ribosomal protein S28-A
+Component #56: nucleic-acid, 5ETS RNA
+Component #57: nucleic-acid, 18S rRNA
+Component #58: nucleic-acid, U3 snoRNA
+Component #59: ligand, ZINC ION
+Component #60: ligand, MAGNESIUM ION
+Component #61: ligand, GUANOSINE-5'-TRIPHOSPHATE
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Sample solution | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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![]() | Microscope: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: OTHER |
Camera | Detector: GATAN K2 SUMMIT (4k x 4k) |
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Image processing
-Atomic model buiding
Output model |
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