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Yorodumi- EMDB-3300: Electron cryo-microscopy of a human pre-ribosomal (pre-40S) particle -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3300 | |||||||||
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Title | Electron cryo-microscopy of a human pre-ribosomal (pre-40S) particle | |||||||||
Map data | Reconstruction of human pre-40S particle purified by using a HASt-tagged version of the ribosome biogenesis factor LTV1 as bait. the map has been filtered and masked using the RELION1.3 postprocess option. | |||||||||
Sample |
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Keywords | ribosome / small subunit precursor / human cells | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 19.4 Å | |||||||||
Authors | Larburu N / Montellese C / O'Donohue M-F / Kutay U / Gleizes P-E / Plisson-Chastang C | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2016 Title: Structure of a human pre-40S particle points to a role for RACK1 in the final steps of 18S rRNA processing. Authors: Natacha Larburu / Christian Montellese / Marie-Françoise O'Donohue / Ulrike Kutay / Pierre-Emmanuel Gleizes / Célia Plisson-Chastang / Abstract: Synthesis of ribosomal subunits in eukaryotes is a complex and tightly regulated process that has been mostly characterized in yeast. The discovery of a growing number of diseases linked to defects ...Synthesis of ribosomal subunits in eukaryotes is a complex and tightly regulated process that has been mostly characterized in yeast. The discovery of a growing number of diseases linked to defects in ribosome biogenesis calls for a deeper understanding of these mechanisms and of the specificities of human ribosome maturation. We present the 19 Å resolution cryo-EM reconstruction of a cytoplasmic precursor to the human small ribosomal subunit, purified by using the tagged ribosome biogenesis factor LTV1 as bait. Compared to yeast pre-40S particles, this first three-dimensional structure of a human 40S subunit precursor shows noticeable differences with respect to the position of ribosome biogenesis factors and uncovers the early deposition of the ribosomal protein RACK1 during subunit maturation. Consistently, RACK1 is required for efficient processing of the 18S rRNA 3'-end, which might be related to its role in translation initiation. This first structural analysis of a human pre-ribosomal particle sets the grounds for high-resolution studies of conformational transitions accompanying ribosomal subunit maturation. | |||||||||
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_3300.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-3300-v30.xml emd-3300.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3300_fsc.xml | 6.6 KB | Display | FSC data file |
Images | emd_3300.tif | 1.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3300 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3300 | HTTPS FTP |
-Validation report
Summary document | emd_3300_validation.pdf.gz | 220.2 KB | Display | EMDB validaton report |
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Full document | emd_3300_full_validation.pdf.gz | 219.3 KB | Display | |
Data in XML | emd_3300_validation.xml.gz | 9.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3300 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3300 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3300.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of human pre-40S particle purified by using a HASt-tagged version of the ribosome biogenesis factor LTV1 as bait. the map has been filtered and masked using the RELION1.3 postprocess option. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : pre-40S particles purified from human cells by using the tagged r...
Entire | Name: pre-40S particles purified from human cells by using the tagged ribosome biogenesis factor HASt_LTV1 as bait. |
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Components |
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-Supramolecule #1000: pre-40S particles purified from human cells by using the tagged r...
Supramolecule | Name: pre-40S particles purified from human cells by using the tagged ribosome biogenesis factor HASt_LTV1 as bait. type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 1.5 MDa |
-Supramolecule #1: cytoplasmic precursor of the human small ribosomal subunit
Supramolecule | Name: cytoplasmic precursor of the human small ribosomal subunit type: complex / ID: 1 / Name.synonym: pre-40S particle / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Tissue: Embryonic Kidney / Cell: HEK 293 |
Molecular weight | Theoretical: 1.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.6 / Details: 10 mM Tris-HCl, 100 mM KCl, 2 mM MgCl2 |
Grid | Details: Glow discharged Quantifoil R2/1 on Cu 300 Mesh grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Method: 1.8 - 2.1'' blot before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Average: 100 K |
Date | Jan 23, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 3812 / Average electron dose: 30 e/Å2 Details: Every image has been acquired in 1s by the direct electron detector (no movies recorded) |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.02 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | The 40S components of pdb model 4V6X were fitted into the pre-40S map by rigid body docking. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |