|Entry||Database: EMDB / ID: 8350|
|Title||Cryo-EM Structure of Yeast Pre-40S, Rio2 Region Local Class "R1"|
|Map data||Pre-40S, Rio2 region local class "R1"|
|Sample||ribosomal small subunit late-stage assembly intermediate:|
|Source||Saccharomyces cerevisiae (baker's yeast)|
|Method||single particle reconstruction / cryo EM / 10.1 Å resolution|
|Authors||Johnson MC / Ghalei H / Doxtader KA / Karbstein K / Stroupe ME|
|Citation||Journal: Structure / Year: 2017|
Title: Structural Heterogeneity in Pre-40S Ribosomes.
Authors: Matthew C Johnson / Homa Ghalei / Katelyn A Doxtader / Katrin Karbstein / M Elizabeth Stroupe
Abstract: Late-stage 40S ribosome assembly is a highly regulated dynamic process that occurs in the cytoplasm, alongside the full translation machinery. Seven assembly factors (AFs) regulate and facilitate ...Late-stage 40S ribosome assembly is a highly regulated dynamic process that occurs in the cytoplasm, alongside the full translation machinery. Seven assembly factors (AFs) regulate and facilitate maturation, but the mechanisms through which they work remain undetermined. Here, we present a series of structures of the immature small subunit (pre-40S) determined by three-dimensional (3D) cryoelectron microscopy with 3D sorting to assess the molecule's heterogeneity. These structures demonstrate an extensive structural heterogeneity of interface AFs that likely regulates subunit joining during 40S maturation. We also present structural models for the beak and the platform, two regions where the low resolution of previous studies did not allow for localization of AFs and the rRNA, respectively. These models are supported by biochemical analyses using point variants and suggest that maturation of the 18S 3' end is regulated by dissociation of the AF Dim1 from the subunit interface, consistent with previous biochemical analyses.
|Date||Deposition: Aug 26, 2016 / Header (metadata) release: Sep 14, 2016 / Map release: Feb 8, 2017 / Last update: Feb 14, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_8350.map.gz (map file in CCP4 format, 67109 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.62 Å|
CCP4 map header:
-Entire ribosomal small subunit late-stage assembly intermediate
|Entire||Name: ribosomal small subunit late-stage assembly intermediate|
Number of components: 1
-Component #1: protein, ribosomal small subunit late-stage assembly intermediate
|Protein||Name: ribosomal small subunit late-stage assembly intermediate|
Recombinant expression: No
|Source||Species: Saccharomyces cerevisiae (baker's yeast)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||pH: 7|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 6 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: DIRECT ELECTRON DE-20 (5k x 3k)|
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi