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Yorodumi- EMDB-1346: The eukaryotic translation initiation factors eIF1 and eIF1A indu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1346 | |||||||||
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Title | The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome. | |||||||||
Map data | Apo 40S | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 21.0 Å | |||||||||
Authors | Passmore LA / Schmeing TM / Maag D / Applefield DJ / Acker MG / Algire MA / Lorsch JR / Ramakrishnan V | |||||||||
Citation | Journal: Mol Cell / Year: 2007 Title: The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome. Authors: Lori A Passmore / T Martin Schmeing / David Maag / Drew J Applefield / Michael G Acker / Mikkel A Algire / Jon R Lorsch / V Ramakrishnan / Abstract: Initiation of translation is the process by which initiator tRNA and the start codon of mRNA are positioned in the ribosomal P site. In eukaryotes, one of the first steps involves the binding of two ...Initiation of translation is the process by which initiator tRNA and the start codon of mRNA are positioned in the ribosomal P site. In eukaryotes, one of the first steps involves the binding of two small factors, eIF1 and eIF1A, to the small (40S) ribosomal subunit. This facilitates tRNA binding, allows scanning of mRNA, and maintains fidelity of start codon recognition. Using cryo-EM, we have obtained 3D reconstructions of 40S bound to both eIF1 and eIF1A, and with each factor alone. These structures reveal that together, eIF1 and eIF1A stabilize a conformational change that opens the mRNA binding channel. Biochemical data reveal that both factors accelerate the rate of ternary complex (eIF2*GTP*Met-tRNA(i)(Met)) binding to 40S but only eIF1A stabilizes this interaction. Our results suggest that eIF1 and eIF1A promote an open, scanning-competent preinitiation complex that closes upon start codon recognition and eIF1 release to stabilize ternary complex binding and clamp down on mRNA. | |||||||||
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_1346.map.gz | 14.2 MB | EMDB map data format | |
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Header (meta data) | emd-1346-v30.xml emd-1346.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | 1346.gif | 89.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1346 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1346 | HTTPS FTP |
-Validation report
Summary document | emd_1346_validation.pdf.gz | 199.1 KB | Display | EMDB validaton report |
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Full document | emd_1346_full_validation.pdf.gz | 198.2 KB | Display | |
Data in XML | emd_1346_validation.xml.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1346 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1346 | 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_1346.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Apo 40S | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.4 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 : S. cerevisiae Apo 40S
Entire | Name: S. cerevisiae Apo 40S |
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Components |
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-Supramolecule #1000: S. cerevisiae Apo 40S
Supramolecule | Name: S. cerevisiae Apo 40S / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 1.2 MDa |
-Supramolecule #1: 40S
Supramolecule | Name: 40S / type: complex / ID: 1 / Name.synonym: small ribosomal subunit / Details: Purified from Saccharomyces 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: 1.2 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: 20 mM HEPES-KOH pH 7.4, 100 mM potassium acetate, 2.5 mM magnesium acetate, 2 mM DTT |
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Grid | Details: Quantifoil R2/2, 200 mesh, Cu/Rh |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 4 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot Method: Samples were diluted to a final concentration of 50 nM or 75 nM immediately before freezing. 4 ul was applied to one side of a glow-discharged grid, blotted on both sides and flash frozen in liquid ethane. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 95 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 200 000X magnification |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6 µm / Number real images: 89 / Average electron dose: 15 e/Å2 Details: Micrographs were digitized using a KZA scanner (MRC, Cambridge). |
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: 5.1 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Particles were manually selected using Ximdisp. |
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CTF correction | Details: Phase flipping |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 29588 |
Final two d classification | Number classes: 490 |
-Atomic model buiding 1
Initial model | PDB ID: 1s1h |
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Software | Name: Situs |
Details | Protocol: rigid body. A model of S. cerevisiae 40S (PDB 1S1H) was manually placed in the density using Chimera and refined as a rigid structure using Situs. |
Refinement | Protocol: RIGID BODY FIT / Target criteria: cross correlation |