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- EMDB-4121: Structure of the 70S ribosome with SECIS-mRNA and P-site tRNA (In... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4121 | |||||||||
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Title | Structure of the 70S ribosome with SECIS-mRNA and P-site tRNA (Initial complex, IC) | |||||||||
![]() | final sharpened map | |||||||||
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![]() | translation / decoding / recoding / selenocysteine / ribosome | |||||||||
Function / homology | ![]() negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Fischer N | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The pathway to GTPase activation of elongation factor SelB on the ribosome. Authors: Niels Fischer / Piotr Neumann / Lars V Bock / Cristina Maracci / Zhe Wang / Alena Paleskava / Andrey L Konevega / Gunnar F Schröder / Helmut Grubmüller / Ralf Ficner / Marina V Rodnina / Holger Stark / ![]() Abstract: In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNA) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNA recodes ...In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNA) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNA recodes a UGA stop codon next to a downstream mRNA stem-loop. Here we present the structures of six intermediates on the pathway of UGA recoding in Escherichia coli by single-particle cryo-electron microscopy. The structures explain the specificity of Sec-tRNA binding by SelB and show large-scale rearrangements of Sec-tRNA. Upon initial binding of SelB-Sec-tRNA to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNA covering the sarcin-ricin loop (SRL) on the 50S subunit. Subsequent codon recognition results in a local closure of the decoding site, which moves Sec-tRNA away from the SRL and triggers a global closure of the 30S subunit shoulder domain. As a consequence, SelB docks on the SRL, activating the GTPase of SelB. These results reveal how codon recognition triggers GTPase activation in translational GTPases. | |||||||||
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 | ![]() | 71.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 72.6 KB 72.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.6 KB | Display | ![]() |
Images | ![]() | 146.1 KB | ||
Filedesc metadata | ![]() | 14.5 KB | ||
Others | ![]() ![]() | 60 MB 60 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lzaMC ![]() 4122C ![]() 4123C ![]() 4124C ![]() 4125C ![]() 4126C ![]() 5lzbC ![]() 5lzcC ![]() 5lzdC ![]() 5lzeC ![]() 5lzfC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 1.0 TB Data #1: Part 1 - Unprocessed cryo-EM micrographs of E. Coli 70S-SelB-GDPNP-Sec-tRNASec-fMet-tRNAfMet-SECIS mRNA complexes [micrographs - single frame] Data #2: Part 2 - Unprocessed cryo-EM micrographs of E. Coli 70S-SelB-GDPNP-Sec-tRNASec-fMet-tRNAfMet-SECIS mRNA complex [micrographs - single frame] Data #3: ribosomeSelB_particles.mrcs - CTF corrected single particle images of E. Coli 70S-SelB-GDPNP-Sec-tRNASec-fMet-tRNAfMet-SECIS mRNA complex [picked particles - multiframe - processed]) |
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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 | final sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: unfiltered half-map 1
File | emd_4121_half_map_1.map | ||||||||||||
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Annotation | unfiltered half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unfiltered half-map 2
File | emd_4121_half_map_2.map | ||||||||||||
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Annotation | unfiltered half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Initial complex, E. coli ribosome 70S-fMet-tRNAfmet-SECIS mRNA co...
+Supramolecule #1: Initial complex, E. coli ribosome 70S-fMet-tRNAfmet-SECIS mRNA co...
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #22: fMet-tRNAfMet
+Macromolecule #23: SECIS mRNA
+Macromolecule #24: 23S ribosomal RNA
+Macromolecule #25: 5S ribosomal RNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein S21
+Macromolecule #26: 50S ribosomal protein L2
+Macromolecule #27: 50S ribosomal protein L3
+Macromolecule #28: 50S ribosomal protein L4
+Macromolecule #29: 50S ribosomal protein L5
+Macromolecule #30: 50S ribosomal protein L6
+Macromolecule #31: 50S ribosomal protein L11
+Macromolecule #32: 50S ribosomal protein L9
+Macromolecule #33: 50S ribosomal protein L13
+Macromolecule #34: 50S ribosomal protein L14
+Macromolecule #35: 50S ribosomal protein L15
+Macromolecule #36: 50S ribosomal protein L16
+Macromolecule #37: 50S ribosomal protein L17
+Macromolecule #38: 50S ribosomal protein L18
+Macromolecule #39: 50S ribosomal protein L19
+Macromolecule #40: 50S ribosomal protein L20
+Macromolecule #41: 50S ribosomal protein L21
+Macromolecule #42: 50S ribosomal protein L22
+Macromolecule #43: 50S ribosomal protein L23
+Macromolecule #44: 50S ribosomal protein L24
+Macromolecule #45: 50S ribosomal protein L25
+Macromolecule #46: 50S ribosomal protein L27
+Macromolecule #47: 50S ribosomal protein L28
+Macromolecule #48: 50S ribosomal protein L29
+Macromolecule #49: 50S ribosomal protein L30
+Macromolecule #50: 50S ribosomal protein L32
+Macromolecule #51: 50S ribosomal protein L33
+Macromolecule #52: 50S ribosomal protein L34
+Macromolecule #53: 50S ribosomal protein L35
+Macromolecule #54: 50S ribosomal protein L36
+Macromolecule #55: 50S ribosomal protein L31
+Macromolecule #56: ZINC ION
-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: 7.5 Details: 50 mM Hepes-KOH, pH 7.5, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6mM spermine, 0.4mM spermidine, 2 mM DTT |
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: CEOS Cs-corrector |
Details | Using a Cs-corrector from CEOS electron optical aberrations were corrected to residual phase errors of 45degree at scattering angles of >12 to 15 mrad. |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 12681 / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | For parts of the model exhibiting larger conformational differences and/or lower local map resolution, additional cycles of real space refinement and manual fitting were performed against experimental map filtered to lower resolution |
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Refinement | Protocol: FLEXIBLE FIT / Target criteria: Maximum likelihood |
Output model | ![]() PDB-5lza: |