|Entry||Database: EMDB / ID: EMD-5905|
|Title||Cryo-EM structure of low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain|
|Sample||Cryo-EM structure of low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain:|
|Keywords||30S subunit assembly / RsgA / RbfA / 17S rRNA processing|
|Biological species||Escherichia coli (E. coli)|
|Method||single particle reconstruction / cryo EM / negative staining / Resolution: 14.4 Å|
|Authors||Yang Z / Guo Q / Goto S / Chen Y / Li N / Yan K / Zhang Y / Muto A / Deng H / Himeno H ...Yang Z / Guo Q / Goto S / Chen Y / Li N / Yan K / Zhang Y / Muto A / Deng H / Himeno H / Lei J / Gao N|
|Citation||Journal: Protein Cell / Year: 2014|
Title: Structural insights into the assembly of the 30S ribosomal subunit in vivo: functional role of S5 and location of the 17S rRNA precursor sequence.
Authors: Zhixiu Yang / Qiang Guo / Simon Goto / Yuling Chen / Ningning Li / Kaige Yan / Yixiao Zhang / Akira Muto / Haiteng Deng / Hyouta Himeno / Jianlin Lei / Ning Gao /
Abstract: The in vivo assembly of ribosomal subunits is a highly complex process, with a tight coordination between protein assembly and rRNA maturation events, such as folding and processing of rRNA ...The in vivo assembly of ribosomal subunits is a highly complex process, with a tight coordination between protein assembly and rRNA maturation events, such as folding and processing of rRNA precursors, as well as modifications of selected bases. In the cell, a large number of factors are required to ensure the efficiency and fidelity of subunit production. Here we characterize the immature 30S subunits accumulated in a factor-null Escherichia coli strain (∆rsgA∆rbfA). The immature 30S subunits isolated with varying salt concentrations in the buffer system show interesting differences on both protein composition and structure. Specifically, intermediates derived under the two contrasting salt conditions (high and low) likely reflect two distinctive assembly stages, the relatively early and late stages of the 3' domain assembly, respectively. Detailed structural analysis demonstrates a mechanistic coupling between the maturation of the 5' end of the 17S rRNA and the assembly of the 30S head domain, and attributes a unique role of S5 in coordinating these two events. Furthermore, our structural results likely reveal the location of the unprocessed terminal sequences of the 17S rRNA, and suggest that the maturation events of the 17S rRNA could be employed as quality control mechanisms on subunit production and protein translation.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_5905.map.gz / Format: CCP4 / Size: 7.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 3 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Cryo-EM structure of low salt treated immature 30S ribosomal subu...
|Entire||Name: Cryo-EM structure of low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain|
Number of components: 1
|Mass||Theoretical: 800 kDa / Experimental: 800 kDa|
-Component #1: ribosome-prokaryote, low salt treated immature 30S ribosomal subu...
|Ribosome-prokaryote||Name: low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain|
a.k.a: immature 30S / Prokaryote: SSU 30S / Recombinant expression: No
|Mass||Theoretical: 800 kDa / Experimental: 800 kDa|
|Source||Species: Escherichia coli (E. coli) / Strain: A19|
|Specimen||Specimen state: Particle / Method: negative staining, cryo EM|
|Sample solution||Buffer solution: 20mM Tris-HCl, 150mM NH4Cl,10mM Mg(OAc)2 / pH: 7.5|
|Support film||Quantifoil 2/4 grids were coated with carbon and glow discharged in a Harrick Plasma Cleaner for 30 seconds|
|Staining||grids were prepared with an FEI Vitrobot Mark IV|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: blot for 1 second before plunging|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Date: Jul 14, 2012|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 8500 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: FEI EAGLE (4k x 4k)|
|Image acquisition||Number of digital images: 4365|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 42521 |
Details: this is a classification volume (NO.3 of five groups) using RELION
|3D reconstruction||Algorithm: reference projection / Software: SPIDER / CTF correction: weiner filter / Resolution: 14.4 Å / Resolution method: FSC 0.5, semi-independent|
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