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Yorodumi- EMDB-11359: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11359 | |||||||||
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Title | Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Pre-A1 | |||||||||
Map data | Multibody refine focus on Platform | |||||||||
Sample |
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Keywords | ribosome / 90S pre-ribosome / 40S pre-ribosome / A1 cleavage / Dhr1 | |||||||||
Function / homology | Function and homology information rRNA cytidine N-acetyltransferase activity / Noc4p-Nop14p complex / rRNA acetylation involved in maturation of SSU-rRNA / box H/ACA snoRNA binding / tRNA N-acetyltransferase activity / regulation of ribosomal protein gene transcription by RNA polymerase II / t-UTP complex / rRNA small subunit pseudouridine methyltransferase Nep1 / tRNA acetylation / RNA fragment catabolic process ...rRNA cytidine N-acetyltransferase activity / Noc4p-Nop14p complex / rRNA acetylation involved in maturation of SSU-rRNA / box H/ACA snoRNA binding / tRNA N-acetyltransferase activity / regulation of ribosomal protein gene transcription by RNA polymerase II / t-UTP complex / rRNA small subunit pseudouridine methyltransferase Nep1 / tRNA acetylation / RNA fragment catabolic process / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / septum digestion after cytokinesis / snRNA binding / tRNA re-export from nucleus / box C/D sno(s)RNA 3'-end processing / regulation of transcription by RNA polymerase I / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / rDNA heterochromatin / positive regulation of rRNA processing / single-stranded telomeric DNA binding / box C/D methylation guide snoRNP complex / tRNA export from nucleus / U4/U6 snRNP / rRNA base methylation / 90S preribosome assembly / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding / SUMOylation of RNA binding proteins / sno(s)RNA-containing ribonucleoprotein complex / protein localization to nucleolus / U4 snRNA binding / O-methyltransferase activity / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / poly(U) RNA binding / U4 snRNP / mRNA modification / U3 snoRNA binding / poly(A)+ mRNA export from nucleus / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / preribosome, small subunit precursor / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / snoRNA binding / precatalytic spliceosome / establishment of cell polarity / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / nucleolar large rRNA transcription by RNA polymerase I / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / 90S preribosome / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / RNA processing / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / vesicle-mediated transport / U4/U6 x U5 tri-snRNP complex / enzyme activator activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA endonuclease activity / nuclear periphery / ribosome assembly / Transferases; Transferring one-carbon groups; Methyltransferases / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / spliceosomal complex / maintenance of translational fidelity / mRNA splicing, via spliceosome / rRNA processing / ribosomal small subunit biogenesis / unfolded protein binding / small ribosomal subunit rRNA binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Cheng J / Lau B | |||||||||
Citation | Journal: Science / Year: 2020 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11359.map.gz | 245.6 MB | EMDB map data format | |
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Header (meta data) | emd-11359-v30.xml emd-11359.xml | 115.4 KB 115.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11359_fsc.xml | 17.1 KB | Display | FSC data file |
Images | emd_11359.png | 176.4 KB | ||
Filedesc metadata | emd-11359.cif.gz | 29.7 KB | ||
Others | emd_11359_additional_1.map.gz emd_11359_additional_2.map.gz emd_11359_additional_3.map.gz emd_11359_additional_4.map.gz | 8.8 MB 10.7 MB 14.7 MB 22.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11359 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11359 | HTTPS FTP |
-Validation report
Summary document | emd_11359_validation.pdf.gz | 513.1 KB | Display | EMDB validaton report |
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Full document | emd_11359_full_validation.pdf.gz | 512.7 KB | Display | |
Data in XML | emd_11359_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | emd_11359_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11359 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11359 | HTTPS FTP |
-Related structure data
Related structure data | 6zqcMC 6zqaC 6zqbC 6zqdC 6zqeC 6zqfC 6zqgC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11359.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Multibody refine focus on Platform | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Additional map: Multibody refine focus on Base
File | emd_11359_additional_1.map | ||||||||||||
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Annotation | Multibody refine focus on Base | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Multibody refine focus on Base
File | emd_11359_additional_2.map | ||||||||||||
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Annotation | Multibody refine focus on Base | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Multibody refine focus on Head
File | emd_11359_additional_3.map | ||||||||||||
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Annotation | Multibody refine focus on Head | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Multibody refine focus on Body
File | emd_11359_additional_4.map | ||||||||||||
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Annotation | Multibody refine focus on Body | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 90S pre-ribbosome state Pre-A1
+Supramolecule #1: 90S pre-ribbosome state Pre-A1
+Macromolecule #1: rRNA 2'-O-methyltransferase fibrillarin
+Macromolecule #2: 40S ribosomal protein S1-A
+Macromolecule #3: RNA cytidine acetyltransferase
+Macromolecule #4: Periodic tryptophan protein 2
+Macromolecule #5: Nucleolar complex protein 14
+Macromolecule #6: Something about silencing protein 10
+Macromolecule #7: U3 small nucleolar RNA-associated protein 4
+Macromolecule #8: U3 small nucleolar RNA-associated protein 5
+Macromolecule #9: U3 small nucleolar RNA-associated protein 6
+Macromolecule #10: U3 small nucleolar RNA-associated protein 7
+Macromolecule #11: U3 small nucleolar RNA-associated protein 8
+Macromolecule #12: U3 small nucleolar RNA-associated protein 9
+Macromolecule #13: U3 small nucleolar RNA-associated protein 10
+Macromolecule #14: U3 small nucleolar RNA-associated protein 11
+Macromolecule #15: U3 small nucleolar RNA-associated protein 12
+Macromolecule #16: U3 small nucleolar RNA-associated protein 13
+Macromolecule #17: U3 small nucleolar RNA-associated protein 14
+Macromolecule #18: U3 small nucleolar RNA-associated protein 15
+Macromolecule #19: Bud site selection protein 21
+Macromolecule #20: NET1-associated nuclear protein 1
+Macromolecule #21: U3 small nucleolar RNA-associated protein 18
+Macromolecule #22: Nucleolar complex protein 4
+Macromolecule #23: U3 small nucleolar RNA-associated protein 20
+Macromolecule #24: U3 small nucleolar RNA-associated protein 21
+Macromolecule #25: U3 small nucleolar RNA-associated protein 22
+Macromolecule #26: rRNA-processing protein FCF1
+Macromolecule #27: Ribosome biogenesis protein UTP30
+Macromolecule #28: Nucleolar protein 56
+Macromolecule #29: Nucleolar protein 58
+Macromolecule #30: 13 kDa ribonucleoprotein-associated protein
+Macromolecule #31: Ribosomal RNA-processing protein 9
+Macromolecule #32: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #33: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #34: U3 small nucleolar RNA-associated protein MPP10
+Macromolecule #35: Ribosome biogenesis protein BMS1
+Macromolecule #36: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #37: Ribosomal RNA-processing protein 7
+Macromolecule #38: Ribosome biogenesis protein ENP2
+Macromolecule #39: Ribosomal RNA small subunit methyltransferase NEP1
+Macromolecule #40: Essential nuclear protein 1
+Macromolecule #41: rRNA biogenesis protein RRP5
+Macromolecule #42: Pre-rRNA-processing protein PNO1
+Macromolecule #43: Protein BFR2
+Macromolecule #44: rRNA-processing protein FCF2
+Macromolecule #45: Protein FAF1
+Macromolecule #46: KRR1 small subunit processome component
+Macromolecule #47: Protein SOF1
+Macromolecule #48: Regulator of rDNA transcription protein 14
+Macromolecule #49: 40S ribosomal protein S4-A
+Macromolecule #50: 40S ribosomal protein S5
+Macromolecule #51: 40S ribosomal protein S6-A
+Macromolecule #52: 40S ribosomal protein S7-A
+Macromolecule #53: 40S ribosomal protein S8-A
+Macromolecule #54: 40S ribosomal protein S9-A
+Macromolecule #55: 40S ribosomal protein S11-A
+Macromolecule #56: 40S ribosomal protein S13
+Macromolecule #57: 40S ribosomal protein S14-A
+Macromolecule #58: 40S ribosomal protein S16-A
+Macromolecule #59: 40S ribosomal protein S18-A
+Macromolecule #60: 40S ribosomal protein S22-A
+Macromolecule #61: 40S ribosomal protein S23-A
+Macromolecule #62: 40S ribosomal protein S24-A
+Macromolecule #63: 40S ribosomal protein S27-A
+Macromolecule #64: 40S ribosomal protein S28-A
+Macromolecule #65: 5ETS RNA
+Macromolecule #66: 18S rRNA
+Macromolecule #67: U3 snoRNA
+Macromolecule #68: ZINC ION
+Macromolecule #69: MAGNESIUM ION
+Macromolecule #70: GUANOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil / Material: COPPER / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-6zqc: |