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Yorodumi- EMDB-1328: Reconfiguration of yeast 40S ribosomal subunit domains by the tra... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1328 | |||||||||
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Title | Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex. | |||||||||
Map data | Reconstruction of the 40S small ribosomal subunit from yeast. | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 19.0 Å | |||||||||
Authors | Gilbert RJC / Gordiyenko Y / von der Haar T | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2007 Title: Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex. Authors: Robert J C Gilbert / Yulya Gordiyenko / Tobias von der Haar / Andreas F-P Sonnen / Gregor Hofmann / Maria Nardelli / David I Stuart / John E G McCarthy / Abstract: In the process of protein synthesis, the small (40S) subunit of the eukaryotic ribosome is recruited to the capped 5' end of the mRNA, from which point it scans along the 5' untranslated region in ...In the process of protein synthesis, the small (40S) subunit of the eukaryotic ribosome is recruited to the capped 5' end of the mRNA, from which point it scans along the 5' untranslated region in search of a start codon. However, the 40S subunit alone is not capable of functional association with cellular mRNA species; it has to be prepared for the recruitment and scanning steps by interactions with a group of eukaryotic initiation factors (eIFs). In budding yeast, an important subset of these factors (1, 2, 3, and 5) can form a multifactor complex (MFC). Here, we describe cryo-EM reconstructions of the 40S subunit, of the MFC, and of 40S complexes with MFC factors plus eIF1A. These studies reveal the positioning of the core MFC on the 40S subunit, and show how eIF-binding induces mobility in the head and platform and reconfigures the head-platform-body relationship. This is expected to increase the accessibility of the mRNA channel, thus enabling the 40S subunit to convert to a recruitment-competent state. | |||||||||
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_1328.map.gz | 756.6 KB | EMDB map data format | |
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Header (meta data) | emd-1328-v30.xml emd-1328.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | 1328.gif | 41.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1328 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1328 | HTTPS FTP |
-Validation report
Summary document | emd_1328_validation.pdf.gz | 201.8 KB | Display | EMDB validaton report |
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Full document | emd_1328_full_validation.pdf.gz | 200.9 KB | Display | |
Data in XML | emd_1328_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1328 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1328 | 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_1328.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the 40S small ribosomal subunit from yeast. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.33 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 : Eukaryotic small ribosomal subunit 40S
Entire | Name: Eukaryotic small ribosomal subunit 40S |
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Components |
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-Supramolecule #1000: Eukaryotic small ribosomal subunit 40S
Supramolecule | Name: Eukaryotic small ribosomal subunit 40S / type: sample / ID: 1000 / Oligomeric state: 40S / Number unique components: 1 |
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Molecular weight | Theoretical: 1.4 MDa |
-Supramolecule #1: Small subunit
Supramolecule | Name: Small subunit / type: complex / ID: 1 / Name.synonym: 40S / Details: S. cerevisiae / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Molecular weight | Experimental: 1.4 MDa / Theoretical: 1.4 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Details: 38mM HEPES, 135mM KAc, 3.25mM MgAc2, 5mM beta-mercaptoethanol, 10uM GMP-PNP |
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Grid | Details: 300 mesh copper grid with lacey carbon film |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home-made plunger Method: Blot with Whatman number 1 paper for 1-2 seconds prior to plunging. |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Temperature | Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Astigmatism corrected at 100,000 x |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 8.33 µm / Number real images: 20 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 2.055 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | The particles were selected manually. |
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CTF correction | Details: Per micrograph |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, FREALIGN, SPIDER, GAP Details: Final maps were computed from CTF-corrected (by phase flipping) images, and scaled in Fourier space to a scattering model of the structure. Number images used: 6267 |
Final angle assignment | Details: SPIDER Euler angle convention |
-Atomic model buiding 1
Software | Name: GAP |
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Details | Protocol: Rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Real space CC and R-factor |