|Entry||Database: EMDB / ID: 1211|
|Title||Hrr25-dependent phosphorylation state regulates organization of the pre-40S subunit.|
|Map data||3D-map of Pre-40S-ribosome|
|Source||Saccharomyces cerevisiae (baker's yeast)|
|Method||single particle reconstruction / cryo EM / 34 Å resolution|
|Authors||Schafer T / Maco B / Petfalski E / Tollervey D / Bottcher B / Aebi U / Hurt E|
|Citation||Journal: Nature / Year: 2006|
Title: Hrr25-dependent phosphorylation state regulates organization of the pre-40S subunit.
Authors: Thorsten Schäfer / Bohumil Maco / Elisabeth Petfalski / David Tollervey / Bettina Böttcher / Ueli Aebi / Ed Hurt
|Date||Deposition: Mar 28, 2006 / Header (metadata) release: Apr 3, 2006 / Map release: Jun 1, 2006 / Last update: Oct 17, 2012|
|Structure viewer||EM map: |
Downloads & links
|File||emd_1211.map.gz (map file in CCP4 format, 2001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 5.72 Å|
CCP4 map header:
-Entire pre-40S ribosome
|Entire||Name: pre-40S ribosome / Oligomeric State: monomer / Number of components: 1|
-Component #1: ribosome-eukaryote, pre-40S ribosome
|Ribosome-eukaryote||Name: pre-40S ribosome|
Details: Ltv1 Tsr1 Enp1 Nob1 Hrr25 Rio2 Dim1 Dim2 Ltv1 used as bait in TAP-purification
Eukaryote: SSU 40S / Recombinant expression: No
|Source||Species: Saccharomyces cerevisiae (baker's yeast)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Buffer solution: 50mM Tris-HCl, 100mM NaCl, 10mM MgCl2, 0.5mM DTT|
|Support film||400 mesh copper rhodium grids (Maxtaform)|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 90 % / Method: Blot for 15 s with Whatman No 1|
Details: Vitrification instrument: Plunger with environmental chamber
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM200FEG|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal) / Astigmatism: bjective lens astigmatism was corrected at / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2200 - 4400 nm|
|Specimen Holder||Holder: Side entry liquid nitrogen-cooled cryo specimen holder|
Model: GATAN LIQUID NITROGEN / Temperature: 94 K
|Camera||Detector: GENERIC CCD|
|Image acquisition||Number of digital images: 69 / Sampling size: 14 microns / Bit depth: 12|
|Processing||Method: single particle reconstruction / Number of class averages: 400 / Number of projections: 4129|
Details: 202 out of 400 classes were used for final reconstruction
Applied symmetry: C1 (asymmetric)
|3D reconstruction||Algorithm: weighted back projection / Software: IMAGIC 5 / CTF correction: Each Particle / Resolution: 34 Å / Resolution method: FSC 0.5 / Euler angles: IMAGIC|
Details: reconstructions were calculated from half of the class averages. Euler angles of class averages were determined by projection matching
-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