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- EMDB-6559: Cryo-electron microscopy structure of ribosome-bound initiation f... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6559 | |||||||||
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Title | Cryo-electron microscopy structure of ribosome-bound initiation factor 2 70S IC II state | |||||||||
![]() | Reconstruction of the 70S-fMet-tRNAiMet-IF2-GDPNP complex, IC II state | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Sprink T / Ramrath DJF / Yamamoto H / Yamamoto K / Loerke J / Ismer J / Hildebrand PW / Scheerer P / Buerger J / Mielke T / Spahn CMT | |||||||||
![]() | ![]() Title: Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association. Authors: Thiemo Sprink / David J F Ramrath / Hiroshi Yamamoto / Kaori Yamamoto / Justus Loerke / Jochen Ismer / Peter W Hildebrand / Patrick Scheerer / Jörg Bürger / Thorsten Mielke / Christian M T Spahn / ![]() Abstract: Throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine ...Throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trGTPase). Although the structural basis for trGTPase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with the ribosome, remains elusive. We determine the structure of IF2 complexed with a nonhydrolyzable guanosine triphosphate analog and initiator fMet-tRNAi (Met) in the context of the Escherichia coli ribosome to 3.7-Å resolution using cryo-electron microscopy. The structural analysis reveals previously unseen intrinsic conformational modes of the 70S initiation complex, establishing the mutual interplay of IF2 and initator transfer RNA (tRNA) with the ribsosome and providing the structural foundation for a mechanistic understanding of the final steps of translation initiation. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 163.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.1 KB 13.1 KB | Display Display | ![]() |
Images | ![]() | 347 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jcjMC ![]() 3285C ![]() 3jcnC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of the 70S-fMet-tRNAiMet-IF2-GDPNP complex, IC II state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.025 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Escherichia coli Initiation Factor 2 stalled on Escherichia coli ...
Entire | Name: Escherichia coli Initiation Factor 2 stalled on Escherichia coli 70S ribosomes by the non-hydrolysable GTP analogue GDPNP in the presence of fMet-tRNAiMet and mRNA |
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Components |
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-Supramolecule #1000: Escherichia coli Initiation Factor 2 stalled on Escherichia coli ...
Supramolecule | Name: Escherichia coli Initiation Factor 2 stalled on Escherichia coli 70S ribosomes by the non-hydrolysable GTP analogue GDPNP in the presence of fMet-tRNAiMet and mRNA type: sample / ID: 1000 / Number unique components: 3 |
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Molecular weight | Experimental: 2.5 MDa / Theoretical: 2.6 MDa |
-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Name.synonym: 70S / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Experimental: 2.5 MDa / Theoretical: 2.6 MDa |
-Macromolecule #1: fMet-tRNAiMet
Macromolecule | Name: fMet-tRNAiMet / type: rna / ID: 1 / Name.synonym: initiator tRNA / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() ![]() |
-Macromolecule #2: Initiation Factor 2
Macromolecule | Name: Initiation Factor 2 / type: protein_or_peptide / ID: 2 / Name.synonym: IF2 / Details: bound to GNPPNP / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Experimental: 97 KDa / Theoretical: 97 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | UniProtKB: Translation initiation factor IF-2 |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Details: 20 mM HEPES-KOH, pH 7.5, 15 mM magnesium acetate, 150 mM potassium acetate, 4 mM 2-mercapthoethanol, 2 mM spermidine, 0.05 mM spermine |
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Grid | Details: Quantifoil R3-3 Cu 300 mesh with 2 nm carbon support film |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I / Method: Blot for 2-4 seconds before plunging. |
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Electron microscopy #1
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 39000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Microscopy ID | 1 |
Date | Aug 26, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 918 / Average electron dose: 20 e/Å2 / Details: Automated data collection using Leginon |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Electron microscopy #2
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 39000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Microscopy ID | 2 |
Date | Jun 10, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 2797 / Average electron dose: 20 e/Å2 / Details: Automated data collection using Leginon |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: CTFFIND4 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: OTHER / Software - Name: EMAN2, CTFFIND4, SPIDER, SPARX Details: Final maps were calculated from two combined datasets. To avoid overfitting, the data were refined in a resolution-limited scheme using SPIDER. Number images used: 54585 |
Details | To avoid overfitting, the data was refined in a resolution-limited scheme using SPIDER. |