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Yorodumi- EMDB-1775: Understanding Ribosome Assembly: the Structure of in vivo Assembl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1775 | |||||||||
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Title | Understanding Ribosome Assembly: the Structure of in vivo Assembled Immature 30S Subunits Revealed by Cryo-electron Microscopy | |||||||||
Map data | Surface rendering of 30S ribosomal subunit from wild type E. coli cells. Map was used as a control. | |||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.1 Å | |||||||||
Authors | Jomaa A / Stewart G / Benito JM / Zielke R / Campbell T / Maddock J / Brown E / Ortega J | |||||||||
Citation | Journal: RNA / Year: 2011 Title: Understanding ribosome assembly: the structure of in vivo assembled immature 30S subunits revealed by cryo-electron microscopy. Authors: Ahmad Jomaa / Geordie Stewart / Jaime Martín-Benito / Ryszard Zielke / Tracey L Campbell / Janine R Maddock / Eric D Brown / Joaquin Ortega / Abstract: Four decades after early in vitro assembly studies demonstrated that ribosome assembly is a controlled process, our understanding of ribosome assembly is still incomplete. Just as structure ...Four decades after early in vitro assembly studies demonstrated that ribosome assembly is a controlled process, our understanding of ribosome assembly is still incomplete. Just as structure determination has been so important to understanding ribosome function, so too will it be critical to sorting out the assembly process. Here, we used a viable deletion in the yjeQ gene, a recognized ribosome assembly factor, to isolate and structurally characterize immature 30S subunits assembled in vivo. These small ribosome subunits contained unprocessed 17S rRNA and lacked some late ribosomal proteins. Cryo-electron microscopy reconstructions revealed that the presence of precursor sequences in the rRNA induces a severe distortion in the 3' minor domain of the subunit involved in the decoding of mRNA and interaction with the large ribosome subunit. These findings suggest that rRNA processing events induce key local conformational changes directing the structure toward the mature assembly. We concluded that rRNA processing, folding, and the entry of tertiary r-proteins are interdependent events in the late stages of 30S subunit assembly. In addition, we demonstrate how studies of emerging assembly factors in ribosome biogenesis can help to elucidate the path of subunit assembly in vivo. | |||||||||
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_1775.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-1775-v30.xml emd-1775.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | 1775.tif | 501.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1775 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1775 | HTTPS FTP |
-Related 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_1775.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Surface rendering of 30S ribosomal subunit from wild type E. coli cells. Map was used as a control. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.54 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 : Reconstruction of the mature 30S subunit from wild type E.coli cells
Entire | Name: Reconstruction of the mature 30S subunit from wild type E.coli cells |
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Components |
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-Supramolecule #1000: Reconstruction of the mature 30S subunit from wild type E.coli cells
Supramolecule | Name: Reconstruction of the mature 30S subunit from wild type E.coli cells type: sample / ID: 1000 Details: The sample was thawed from storage at -80 degrees Celcius before being loaded onto the grid. Number unique components: 1 |
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Molecular weight | Theoretical: 800 KDa |
-Supramolecule #1: Small Ribosomal Subunit
Supramolecule | Name: Small Ribosomal Subunit / type: complex / ID: 1 / Name.synonym: 30S / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: SSU 30S |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 850 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.8 mg/mL |
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Buffer | pH: 7.5 Details: 10 mM Tris-HCl pH 7.5, 10 mM magnesium acetate, 60 mM NH4Cl, 3 mM 2-mercaptoethanol |
Grid | Details: 400 Mesh Copper Grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: OTHER / Details: Vitrification instrument: FEI vitrobot / Method: Blot 7 Seconds Twice |
-Electron microscopy
Microscope | JEOL 2010F |
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Temperature | Min: 93 K / Max: 93 K / Average: 93 K |
Date | Dec 10, 2008 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 12.7 µm / Number real images: 29 / Average electron dose: 10 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.0 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.65 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder. Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | Particles were picked with BOXER |
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CTF correction | Details: Each Micrograph |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp / Number images used: 25803 |
-Atomic model buiding 1
Initial model | PDB ID: 2z4k |
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Software | Name: Situs |
Details | Protocol: Rigid Body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |