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- EMDB-10054: Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaet... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10054 | |||||||||
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Title | Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state C | |||||||||
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![]() | 90S pre-ribosome, state C
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Function / homology | ![]() rRNA cytidine N-acetyltransferase activity / tRNA acetylation / mRNA modification / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / rRNA modification / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex ...rRNA cytidine N-acetyltransferase activity / tRNA acetylation / mRNA modification / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / rRNA modification / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Cheng J / Kellner N / Griesel S / Berninghausen O / Beckmann R / Hurt E | |||||||||
![]() | ![]() Title: Thermophile 90S Pre-ribosome Structures Reveal the Reverse Order of Co-transcriptional 18S rRNA Subdomain Integration. Authors: Jingdong Cheng / Jochen Baßler / Paulina Fischer / Benjamin Lau / Nikola Kellner / Ruth Kunze / Sabine Griesel / Martina Kallas / Otto Berninghausen / Daniela Strauss / Roland Beckmann / Ed Hurt / ![]() Abstract: Eukaryotic ribosome biogenesis involves RNA folding and processing that depend on assembly factors and small nucleolar RNAs (snoRNAs). The 90S (SSU-processome) is the earliest pre-ribosome ...Eukaryotic ribosome biogenesis involves RNA folding and processing that depend on assembly factors and small nucleolar RNAs (snoRNAs). The 90S (SSU-processome) is the earliest pre-ribosome structurally analyzed, which was suggested to assemble stepwise along the growing pre-rRNA from 5' > 3', but this directionality may not be accurate. Here, by analyzing the structure of a series of 90S assembly intermediates from Chaetomium thermophilum, we discover a reverse order of 18S rRNA subdomain incorporation. Large parts of the 18S rRNA 3' and central domains assemble first into the 90S before the 5' domain is integrated. This final incorporation depends on a contact between a heterotrimer Enp2-Bfr2-Lcp5 recruited to the flexible 5' domain and Kre33, which reconstitutes the Kre33-Enp-Brf2-Lcp5 module on the compacted 90S. Keeping the 5' domain temporarily segregated from the 90S scaffold could provide extra time to complete the multifaceted 5' domain folding, which depends on a distinct set of snoRNAs and processing factors. | |||||||||
Validation Report | PDB-ID: 6rxx![]() ![]() ![]() | |||||||||
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 | ![]() 6rxxCM ![]() 6rxtC ![]() 6rxuC ![]() 6rxvC ![]() 6rxyC ![]() 6rxzC 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: 1.084 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-ribosome, state C
+Component #1: protein, 90S pre-ribosome, state C
+Component #2: protein, Periodic tryptophan protein 2-like protein
+Component #3: protein, Utp3
+Component #4: protein, Utp6
+Component #5: protein, Utp7
+Component #6: protein, U3 small nucleolar RNA-associated protein 11
+Component #7: protein, Utp12
+Component #8: protein, Utp13
+Component #9: protein, Utp14
+Component #10: protein, Utp18
+Component #11: protein, Putative U3 snoRNP protein
+Component #12: protein, Utp24
+Component #13: protein, Imp3
+Component #14: protein, Putative U3 small nucleolar ribonucleoprotein
+Component #15: protein, Putative U3 small nucleolar ribonucleoprotein protein
+Component #16: protein, Sof1
+Component #17: protein, Emg1
+Component #18: protein, KRR1 small subunit processome component
+Component #19: protein, Pre-rRNA-processing protein PNO1
+Component #20: protein, 40S ribosomal protein S1
+Component #21: protein, 40S ribosomal protein s5-like protein
+Component #22: protein, 40S ribosomal protein S7
+Component #23: protein, 40S ribosomal protein s9-like protein
+Component #24: protein, 40S ribosomal protein S13-like protein
+Component #25: protein, 40S ribosomal protein S14-like protein
+Component #26: protein, 40S ribosomal protein S16-like protein
+Component #27: protein, 40S ribosomal protein S22-like protein
+Component #28: protein, 40S ribosomal protein s23-like protein
+Component #29: protein, 40S ribosomal protein S28-like protein
+Component #30: protein, Ribosomal protein s27-like protein
+Component #31: protein, Faf1
+Component #32: nucleic-acid, 35S ribosomal RNA
+Component #33: protein, U3 small nucleolar RNA-associated protein 22
+Component #34: protein, Rrp7
+Component #35: protein, Putative ribosomal protein
+Component #36: protein, RNA 3'-terminal phosphate cyclase-like protein
+Component #37: protein, Bms1
+Component #38: protein, Kre33
+Component #39: protein, 40S ribosomal protein S4
+Component #40: protein, 40S ribosomal protein S6
+Component #41: protein, 40S ribosomal protein S8
+Component #42: protein, 40S ribosomal protein S11-like protein
+Component #43: protein, 40S ribosomal protein S24
+Component #44: protein, Ribosome biogenesis protein ENP2
+Component #45: protein, Utp20
+Component #46: protein, Bfr2
+Component #47: protein, Utp2
+Component #48: protein, Utp4
+Component #49: protein, UTP10
+Component #50: protein, Utp15
+Component #51: protein, Utp17
+Component #52: protein, Enp1
+Component #53: protein, Utp5
+Component #54: protein, Utp16
+Component #55: protein, Utp8
+Component #56: protein, Noc4
+Component #57: protein, Nop1
+Component #58: protein, Putative nucleolar protein
+Component #59: protein, Nop58
+Component #60: protein, Snu13
+Component #61: protein, Rrp9
+Component #62: protein, Fcf2
+Component #63: nucleic-acid, U3 snoRNA
+Component #64: protein, 40S ribosomal protein S19-like protein
+Component #65: ligand, ZINC ION
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Sample solution | pH: 7.5 |
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: FEI FALCON II (4k x 4k) |
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Image processing
-Atomic model buiding
Output model |
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