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- EMDB-1249: The cryo-EM structure of a translation initiation complex from Es... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1249 | |||||||||
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Title | The cryo-EM structure of a translation initiation complex from Escherichia coli. | |||||||||
![]() | This is a difference map, which reveals the non-ribosomal components of the E. coli 70S initiation complex. | |||||||||
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Function / homology | ![]() guanosine tetraphosphate binding / ribosomal small subunit binding / chaperone-mediated protein folding / translation initiation factor activity / response to cold / translational initiation / ribosome binding / rRNA binding / GTPase activity / GTP binding ...guanosine tetraphosphate binding / ribosomal small subunit binding / chaperone-mediated protein folding / translation initiation factor activity / response to cold / translational initiation / ribosome binding / rRNA binding / GTPase activity / GTP binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.8 Å | |||||||||
![]() | Allen GS / Zavialov A / Gursky R / Ehrenberg M / Frank J | |||||||||
![]() | ![]() Title: The cryo-EM structure of a translation initiation complex from Escherichia coli. Authors: Gregory S Allen / Andrey Zavialov / Richard Gursky / Måns Ehrenberg / Joachim Frank / ![]() Abstract: The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex ...The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex (IC) stalled after 70S assembly. We have obtained a cryo-EM reconstruction of the IC showing IF2*GDPNP at the intersubunit cleft of the 70S ribosome. IF2*GDPNP contacts the 30S and 50S subunits as well as fMet-tRNA(fMet). IF2 here adopts a conformation radically different from that seen in the recent crystal structure of IF2. The C-terminal domain of IF2 binds to the single-stranded portion of fMet-tRNA(fMet), thereby forcing the tRNA into a novel orientation at the P site. The GTP binding domain of IF2 binds to the GTPase-associated center of the 50S subunit in a manner similar to EF-G and EF-Tu. Additionally, we present evidence for the localization of IF1, IF3, one C-terminal domain of L7/L12, and the N-terminal domain of IF2 in the initiation complex. | |||||||||
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 | ![]() | 8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.6 KB 11.6 KB | Display Display | ![]() |
Images | ![]() | 20.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 279.1 KB | Display | ![]() |
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Full document | ![]() | 278.7 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zo1MC ![]() 1zo3MC ![]() 1248C 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a difference map, which reveals the non-ribosomal components of the E. coli 70S initiation complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.82 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 : E. coli 70S, IF1, IF3, mRNA, fMet-tRNA, and IF2-GDPNP
Entire | Name: E. coli 70S, IF1, IF3, mRNA, fMet-tRNA, and IF2-GDPNP |
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Components |
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-Supramolecule #1000: E. coli 70S, IF1, IF3, mRNA, fMet-tRNA, and IF2-GDPNP
Supramolecule | Name: E. coli 70S, IF1, IF3, mRNA, fMet-tRNA, and IF2-GDPNP / type: sample / ID: 1000 / Oligomeric state: One of each component binds to the 70S / Number unique components: 7 |
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-Macromolecule #1: fmet-tRNA
Macromolecule | Name: fmet-tRNA / type: rna / ID: 1 / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #5: mRNA
Macromolecule | Name: mRNA / type: rna / ID: 5 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #2: beta IF2-GDPNP
Macromolecule | Name: beta IF2-GDPNP / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #3: IF1
Macromolecule | Name: IF1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #4: IF3
Macromolecule | Name: IF3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 / Details: polymix buffer |
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Grid | Details: Quantifoil |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: 2 second blot |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Average: 80 K |
Date | Jul 4, 2003 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 116 / Od range: 1.2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 39000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.93 µm / Nominal defocus min: 0.93 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: cryo stage / Specimen holder model: GATAN HELIUM |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Image processing
Details | automated particle picking followed by manual verification |
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CTF correction | Details: defocus groups |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER Details: This volume is a difference map constructed by the subtraction of a post-initiation map from the initiation map emd-1248. Number images used: 20283 |
-Atomic model buiding 1
Software | Name: RSRef |
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Details | Protocol: real-space refinement of rigid bodies. IF2, P/I site tRNA, and IF1 were initially fit by hand in O then refined by RSRef. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient |
Output model | ![]() PDB-1zo1: ![]() PDB-1zo3: |