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- EMDB-6695: Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-dep... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6695 | |||||||||
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Title | Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1) | |||||||||
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![]() | 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP)
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Function / homology | ![]() CURI complex / t-UTP complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Pwp2p-containing subcomplex of 90S preribosome / sno(s)RNA processing / RNA fragment catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ye K / Zhu X / Sun Q | |||||||||
![]() | ![]() Title: Molecular architecture of the 90S small subunit pre-ribosome. Authors: Qi Sun / Xing Zhu / Jia Qi / Weidong An / Pengfei Lan / Dan Tan / Rongchang Chen / Bing Wang / Sanduo Zheng / Cheng Zhang / Xining Chen / Wei Zhang / Jing Chen / Meng-Qiu Dong / Keqiong Ye / ![]() Abstract: Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the ...Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors. | |||||||||
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 | ![]() 5wyjCM ![]() 6696C ![]() 6697C ![]() 5wwnC ![]() 5wwoC ![]() 5wxlC ![]() 5wxmC ![]() 5wy3C ![]() 5wykC ![]() 5wylC 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: 1.76 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 small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP)
+Component #1: protein, 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP)
+Component #2: nucleic-acid, U3 RNA
+Component #3: protein, rRNA 2'-O-methyltransferase fibrillarin
+Component #4: protein, Nucleolar protein 56
+Component #5: protein, Nucleolar protein 58
+Component #6: protein, Ribosomal RNA-processing protein 9
+Component #7: protein, 13 kDa ribonucleoprotein-associated protein
+Component #8: nucleic-acid, 5ETS RNA
+Component #9: protein, Utp4
+Component #10: protein, Utp5
+Component #11: protein, Utp8
+Component #12: protein, Utp9
+Component #13: protein, U3 small nucleolar RNA-associated protein 10,Utp10
+Component #14: protein, Utp15
+Component #15: protein, Utp17
+Component #16: protein, Ribosome biogenesis protein BMS1
+Component #17: protein, Periodic tryptophan protein 2
+Component #18: protein, U3 small nucleolar RNA-associated protein 12
+Component #19: protein, U3 small nucleolar RNA-associated protein 13
+Component #20: protein, U3 small nucleolar RNA-associated protein 18
+Component #21: protein, U3 small nucleolar RNA-associated protein 21
+Component #22: protein, Ribosomal RNA-processing protein 7
+Component #23: protein, U3 small nucleolar RNA-associated protein 22
+Component #24: protein, Ribosomal RNA small subunit methyltransferase NEP1
+Component #25: protein, Essential nuclear protein 1
+Component #26: protein, Enp2
+Component #27: protein, KRR1 small subunit processome component
+Component #28: protein, U3 small nucleolar ribonucleoprotein protein IMP3
+Component #29: protein, U3 small nucleolar ribonucleoprotein protein IMP4
+Component #30: protein, Mpp10,U3 small nucleolar RNA-associated protein MPP10
+Component #31: protein, Pre-rRNA-processing protein PNO1
+Component #32: protein, RNA 3'-terminal phosphate cyclase-like protein
+Component #33: protein, rRNA biogenesis protein RRP5
+Component #34: protein, Sof1
+Component #35: nucleic-acid, 18S ribosomal RNA
+Component #36: protein, 40S ribosomal protein S1-A
+Component #37: protein, 40S ribosomal protein S4-A
+Component #38: protein, 40S ribosomal protein S5
+Component #39: protein, 40S ribosomal protein S6-A
+Component #40: protein, 40S ribosomal protein S7-A
+Component #41: protein, 40S ribosomal protein S8-A
+Component #42: protein, 40S ribosomal protein S9-A
+Component #43: protein, 40S ribosomal protein S11-A
+Component #44: protein, 40S ribosomal protein S12
+Component #45: protein, 40S ribosomal protein S13
+Component #46: protein, 40S ribosomal protein S14-A
+Component #47: protein, 40S ribosomal protein S16-A
+Component #48: protein, 40S ribosomal protein S22-A
+Component #49: protein, 40S ribosomal protein S23-A
+Component #50: protein, 40S ribosomal protein S24-A
+Component #51: protein, 40S ribosomal protein S27-A
+Component #52: protein, 40S ribosomal protein S28-A
+Component #53: protein, 40S ribosomal protein S30-A
+Component #54: protein, Ubiquitin-40S ribosomal protein S31
+Component #55: protein, Utp7
+Component #56: protein, Utp11
+Component #57: protein, Utp20
+Component #58: protein, rRNA-processing protein FCF1
+Component #59: protein, Ribosome biogenesis protein UTP30
+Component #60: protein, Helical domain protein
+Component #61: protein, Helical domain protein
+Component #62: protein, Unassigned helices
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Sample solution | pH: 8 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 % |
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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 | Magnification: 45000.0 X (nominal), 79545.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: FEI TITAN KRIOS AUTOGRID HOLDER |
Camera | Detector: OTHER |
-Image acquisition
Image acquisition | Number of digital images: 2055 |
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Image processing
-Atomic model buiding
Output model |
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