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- EMDB-2620: POST-translocational 80S ribosomal state of Regulation of the mam... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2620 | |||||||||
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Title | POST-translocational 80S ribosomal state of Regulation of the mammalian elongation cycle by 40S subunit rolling: a eukaryotic-specific ribosome rearrangement | |||||||||
![]() | reconstruction of post-translocational 80S state | |||||||||
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![]() | translation / mammalian 80S ribosome / elongation cycle / post-translocational state / tRNA selection / cryo-electron microscopy | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.9 Å | |||||||||
![]() | Budkevich TV / Giesebrecht J / Behrmann E / Loerke J / Ramrath D / Mielke T / Ismer J / Hildebrand P / Tung C-S / Nierhaus KH ...Budkevich TV / Giesebrecht J / Behrmann E / Loerke J / Ramrath D / Mielke T / Ismer J / Hildebrand P / Tung C-S / Nierhaus KH / Sanbonmatsu KY / Spahn CMT | |||||||||
![]() | ![]() Title: Regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement. Authors: Tatyana V Budkevich / Jan Giesebrecht / Elmar Behrmann / Justus Loerke / David J F Ramrath / Thorsten Mielke / Jochen Ismer / Peter W Hildebrand / Chang-Shung Tung / Knud H Nierhaus / ...Authors: Tatyana V Budkevich / Jan Giesebrecht / Elmar Behrmann / Justus Loerke / David J F Ramrath / Thorsten Mielke / Jochen Ismer / Peter W Hildebrand / Chang-Shung Tung / Knud H Nierhaus / Karissa Y Sanbonmatsu / Christian M T Spahn / ![]() ![]() ![]() Abstract: The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution ...The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80S ribosome in the posttranslocational state and in complex with the eukaryotic eEF1A⋅Val-tRNA⋅GMPPNP ternary complex, revealing significant differences in the elongation mechanism between bacteria and mammals. Surprisingly, and in contrast to bacterial ribosomes, a rotation of the small subunit around its long axis and orthogonal to the well-known intersubunit rotation distinguishes the posttranslocational state from the classical pretranslocational state ribosome. We term this motion "subunit rolling." Correspondingly, a mammalian decoding complex visualized in substates before and after codon recognition reveals structural distinctions from the bacterial system. These findings suggest how codon recognition leads to GTPase activation in the mammalian system and demonstrate that in mammalia subunit rolling occurs during tRNA selection. | |||||||||
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 | ![]() | 154.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.3 KB 12.3 KB | Display Display | ![]() |
Images | ![]() | 732.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ujeMC ![]() 2621C ![]() 2622C ![]() 2623C ![]() 2624C ![]() 4cxgC ![]() 4cxhC 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 | reconstruction of post-translocational 80S state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.26 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 : POST-translocational rabbit 80S ribosome with two tRNAs and mRNA bound
Entire | Name: POST-translocational rabbit 80S ribosome with two tRNAs and mRNA bound |
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Components |
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-Supramolecule #1000: POST-translocational rabbit 80S ribosome with two tRNAs and mRNA bound
Supramolecule | Name: POST-translocational rabbit 80S ribosome with two tRNAs and mRNA bound type: sample / ID: 1000 Details: 80S were re-associated from 40S and 60S subunits and the sample prepared in vitro from individual components Oligomeric state: Two tRNAs and one mRNA bound to one 80S ribosome Number unique components: 4 |
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Molecular weight | Theoretical: 4.5 MDa |
-Supramolecule #1: re-associated 80S
Supramolecule | Name: re-associated 80S / type: complex / ID: 1 / Name.synonym: 80S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 4.5 MDa |
-Macromolecule #1: transfer RNA
Macromolecule | Name: transfer RNA / type: rna / ID: 1 / Name.synonym: tRNA / Details: tRNAPhe / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25 KDa |
-Macromolecule #2: messenger RNA
Macromolecule | Name: messenger RNA / type: rna / ID: 2 / Name.synonym: mRNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 14.1 KDa |
Sequence | String: GGGAAAAGAA AAGAAAAGAA AAUGUUCAAA GAAAAGAAAA GAAAU |
-Macromolecule #3: transfer RNA
Macromolecule | Name: transfer RNA / type: rna / ID: 3 / Name.synonym: tRNA / Details: tRNALys, isoacceptor 3 / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25 KDa |
Sequence | String: GCCCGGAUAG CUCAGUCGGU AGAGCAUCAG ACUUUUUAUC UGAGGGUCCA GGGUUCAGUC CCUGUUCGGG CGCCA |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.38 mg/mL |
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Buffer | pH: 7.5 Details: 20mM Hepes-KOH, 5mM MgCl2,100 mM NH4Cl, 6 mM beta-mercaptoethanol, 0.8 mM spermidine, 0.6 mM spermine |
Grid | Details: Quantifoil grids with additional continuous carbon support. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Instrument: FEI VITROBOT MARK II / Method: blot for 2/4 seconds before plunging |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 77 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification |
Details | minimal dose system |
Date | Jun 2, 2008 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Number real images: 826 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 65520 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Details | The particles were selected using SIGNATURE and processed by using SPIDER and SPARX. |
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CTF correction | Details: defocus group |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: OTHER / Software - Name: Spider, Sparx / Number images used: 236113 |