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Yorodumi- EMDB-9964: 3.4 angstrom cryo-EM structure of yeast 90S small subunit preribosome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9964 | |||||||||
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Title | 3.4 angstrom cryo-EM structure of yeast 90S small subunit preribosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ribosome assembly / 90S pre-ribosome / cryo-EM / Mtr4 / Ribosome | |||||||||
Function / homology | Function and homology information rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / mRNA modification / Noc4p-Nop14p complex / tRNA acetylation / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / RNA fragment catabolic process / CURI complex ...rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / mRNA modification / Noc4p-Nop14p complex / tRNA acetylation / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / RNA fragment catabolic process / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA modification / septum digestion after cytokinesis / snRNA binding / positive regulation of RNA binding / SUMOylation of RNA binding proteins / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / regulation of transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / rRNA methyltransferase activity / positive regulation of rRNA processing / box C/D methylation guide snoRNP complex / U4/U6 snRNP / rRNA base methylation / single-stranded telomeric DNA binding / rRNA primary transcript binding / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / protein localization to nucleolus / O-methyltransferase activity / U4 snRNP / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / U3 snoRNA binding / : / poly(A)+ mRNA export from nucleus / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / precatalytic spliceosome / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / snoRNA binding / spliceosomal complex assembly / establishment of cell polarity / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / enzyme activator activity / 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) / regulation of translational fidelity / RNA processing / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / RNA endonuclease activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Transferases; Transferring one-carbon groups; Methyltransferases / nuclear periphery / small-subunit processome / maintenance of translational fidelity / spliceosomal complex / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / mRNA splicing, via spliceosome / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / cell cycle / translation Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) / Saccharomyces cerevisiae S288C (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Du Y / Ye K | |||||||||
Funding support | China, 2 items
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Citation | Journal: To be published Title: 3.4 angstrom cryo-EM structure of yeast 90S small subunit preribosome Authors: Du Y / An W / Qi S / Ye K | |||||||||
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_9964.map.gz | 53.2 MB | EMDB map data format | |
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Header (meta data) | emd-9964-v30.xml emd-9964.xml | 121.3 KB 121.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9964_fsc.xml | 17.9 KB | Display | FSC data file |
Images | emd_9964.png | 71.6 KB | ||
Filedesc metadata | emd-9964.cif.gz | 29.5 KB | ||
Others | emd_9964_additional_1.map.gz emd_9964_additional_2.map.gz emd_9964_additional_3.map.gz emd_9964_additional_4.map.gz emd_9964_additional_5.map.gz | 70.2 MB 14.8 MB 42.4 MB 18.6 MB 44.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9964 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9964 | HTTPS FTP |
-Related structure data
Related structure data | 6ke6MC 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_9964.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: 3' major domain map
File | emd_9964_additional_1.map | ||||||||||||
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Annotation | 3' major domain map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 5' domain map
File | emd_9964_additional_2.map | ||||||||||||
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Annotation | 5' domain map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: UTPA map
File | emd_9964_additional_3.map | ||||||||||||
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Annotation | UTPA map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Central domain map
File | emd_9964_additional_4.map | ||||||||||||
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Annotation | Central domain map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Core map
File | emd_9964_additional_5.map | ||||||||||||
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Annotation | Core map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 90S pre-ribosome (Mtr4-depleted, Enp1-TAP)
+Supramolecule #1: 90S pre-ribosome (Mtr4-depleted, Enp1-TAP)
+Macromolecule #1: U3 snoRNA
+Macromolecule #2: 5' ETS
+Macromolecule #3: 18S rRNA
+Macromolecule #4: 40S ribosomal protein S1-A
+Macromolecule #5: 40S ribosomal protein S4-A
+Macromolecule #6: 40S ribosomal protein S5
+Macromolecule #7: 40S ribosomal protein S6-A
+Macromolecule #8: 40S ribosomal protein S7-A
+Macromolecule #9: 40S ribosomal protein S8-A
+Macromolecule #10: 40S ribosomal protein S9-A
+Macromolecule #11: 40S ribosomal protein S11-A
+Macromolecule #12: 40S ribosomal protein S12
+Macromolecule #13: 40S ribosomal protein S13
+Macromolecule #14: 40S ribosomal protein S14-A
+Macromolecule #15: 40S ribosomal protein S16-A
+Macromolecule #16: 40S ribosomal protein S18-A
+Macromolecule #17: 40S ribosomal protein S22-B
+Macromolecule #18: 40S ribosomal protein S23-A
+Macromolecule #19: 40S ribosomal protein S24-A
+Macromolecule #20: 40S ribosomal protein S27-A
+Macromolecule #21: 40S ribosomal protein S28-A
+Macromolecule #22: rRNA 2'-O-methyltransferase fibrillarin
+Macromolecule #23: Nucleolar protein 56
+Macromolecule #24: Nucleolar protein 58
+Macromolecule #25: Ribosomal RNA-processing protein 9
+Macromolecule #26: 13 kDa ribonucleoprotein-associated protein
+Macromolecule #27: U3 small nucleolar RNA-associated protein 4
+Macromolecule #28: U3 small nucleolar RNA-associated protein 5
+Macromolecule #29: U3 small nucleolar RNA-associated protein 8
+Macromolecule #30: U3 small nucleolar RNA-associated protein 9
+Macromolecule #31: U3 small nucleolar RNA-associated protein 10
+Macromolecule #32: U3 small nucleolar RNA-associated protein 15
+Macromolecule #33: NET1-associated nuclear protein 1
+Macromolecule #34: Periodic tryptophan protein 2
+Macromolecule #35: U3 small nucleolar RNA-associated protein 12
+Macromolecule #36: U3 small nucleolar RNA-associated protein 13
+Macromolecule #37: U3 small nucleolar RNA-associated protein 18
+Macromolecule #38: U3 small nucleolar RNA-associated protein 21
+Macromolecule #39: U3 small nucleolar RNA-associated protein 6
+Macromolecule #40: Bud site selection protein 21
+Macromolecule #41: U3 small nucleolar RNA-associated protein 7
+Macromolecule #42: U3 small nucleolar RNA-associated protein 11
+Macromolecule #43: U3 small nucleolar RNA-associated protein MPP10
+Macromolecule #44: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #45: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #46: Something about silencing protein 10
+Macromolecule #47: Protein SOF1
+Macromolecule #48: rRNA-processing protein FCF2
+Macromolecule #49: rRNA-processing protein FCF1
+Macromolecule #50: Ribosome biogenesis protein ENP2
+Macromolecule #51: U3 small nucleolar ribonucleoprotein protein LCP5
+Macromolecule #52: KRR1 small subunit processome component
+Macromolecule #53: U3 small nucleolar RNA-associated protein 22
+Macromolecule #54: Ribosomal RNA-processing protein 7
+Macromolecule #55: Ribosomal RNA small subunit methyltransferase NEP1
+Macromolecule #56: Ribosome biogenesis protein UTP30
+Macromolecule #57: Ribosome biogenesis protein BMS1
+Macromolecule #58: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #59: RNA cytidine acetyltransferase
+Macromolecule #60: Nucleolar complex protein 14
+Macromolecule #61: Nucleolar complex protein 4
+Macromolecule #62: U3 small nucleolar RNA-associated protein 20
+Macromolecule #63: U3 small nucleolar RNA-associated protein 14
+Macromolecule #64: Essential nuclear protein 1
+Macromolecule #65: Pre-rRNA-processing protein PNO1
+Macromolecule #66: Protein FAF1
+Macromolecule #67: Unassigned helices
+Macromolecule #68: ZINC ION
+Macromolecule #69: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #70: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.0 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: wait 30s and blot 2s before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 25000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number grids imaged: 3 / Number real images: 4723 / Average exposure time: 9.3 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |