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- EMDB-0058: Cryo-EM map of a partial yeast 48S preinitiation complex in its c... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0058 | |||||||||
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Title | Cryo-EM map of a partial yeast 48S preinitiation complex in its closed conformation obtained by focused classification using masks for eIF3b-eIF3i. | |||||||||
![]() | For optimal visualization of eIF2, and of eIF3c, eIF3b and eIf3a c-term at the subunit interface, gauss-filter the map by 1.34 and display it at 0.035 | |||||||||
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![]() | ribosome / translation / initiation factors / 40S / eIF1A / eIF3 / eIF2 / tRNAi / 48S PIC / small ribosome subunit | |||||||||
Function / homology | ![]() formation of translation initiation ternary complex / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / incipient cellular bud site / eukaryotic translation initiation factor 2 complex ...formation of translation initiation ternary complex / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / incipient cellular bud site / eukaryotic translation initiation factor 2 complex / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / positive regulation of translational fidelity / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / regulation of translational fidelity / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation initiation factor binding / translation initiation factor activity / rescue of stalled ribosome / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / double-stranded RNA binding / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / protein kinase binding / RNA binding / zinc ion binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.75 Å | |||||||||
![]() | Llacer JL / Hussain T | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex. Authors: Jose L Llácer / Tanweer Hussain / Laura Marler / Colin Echeverría Aitken / Anil Thakur / Jon R Lorsch / Alan G Hinnebusch / V Ramakrishnan / ![]() ![]() Abstract: Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and ...Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition. | |||||||||
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 | ![]() | 96.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 83.2 KB 83.2 KB | Display Display | ![]() |
Images | ![]() | 75.3 KB | ||
Filedesc metadata | ![]() | 15.6 KB | ||
Others | ![]() ![]() | 80.8 MB 80.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gsnMC ![]() 0057C ![]() 6gsmC 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 | For optimal visualization of eIF2, and of eIF3c, eIF3b and eIf3a c-term at the subunit interface, gauss-filter the map by 1.34 and display it at 0.035 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_0058_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_0058_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Structure of a partial yeast 48S preinitiation complex in closed ...
+Supramolecule #1: Structure of a partial yeast 48S preinitiation complex in closed ...
+Supramolecule #3: tRNA
+Supramolecule #4: Initiation factors
+Supramolecule #5: mRNA
+Supramolecule #6: Initiation factors
+Supramolecule #2: Ribosome
+Macromolecule #1: 18S rRNA (1798-MER)
+Macromolecule #20: mRNA
+Macromolecule #28: tRNAi (75-MER)
+Macromolecule #2: KLLA0F09812p
+Macromolecule #3: KLLA0D08305p
+Macromolecule #4: KLLA0D10659p
+Macromolecule #5: KLLA0B08173p
+Macromolecule #6: 40S ribosomal protein S12
+Macromolecule #7: KLLA0F07843p
+Macromolecule #8: 40S ribosomal protein S16
+Macromolecule #9: KLLA0B01474p
+Macromolecule #10: KLLA0B01562p
+Macromolecule #11: KLLA0A07194p
+Macromolecule #12: KLLA0F25542p
+Macromolecule #13: KLLA0B06182p
+Macromolecule #14: 40S ribosomal protein S28
+Macromolecule #15: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #16: KLLA0E12277p
+Macromolecule #17: 40S ribosomal protein S29
+Macromolecule #18: 40S ribosomal protein S30
+Macromolecule #19: 60S ribosomal protein L41-A
+Macromolecule #21: Eukaryotic translation initiation factor 1A
+Macromolecule #22: Eukaryotic translation initiation factor eIF-1
+Macromolecule #23: Eukaryotic translation initiation factor 3 subunit A,eIF3a
+Macromolecule #24: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #25: Eukaryotic translation initiation factor 2 subunit gamma
+Macromolecule #26: Eukaryotic translation initiation factor 2 subunit beta
+Macromolecule #27: Eukaryotic translation initiation factor 2 subunit alpha
+Macromolecule #29: 40S ribosomal protein S0
+Macromolecule #30: 40S ribosomal protein S1
+Macromolecule #31: 40S ribosomal protein S4
+Macromolecule #32: 40S ribosomal protein S6
+Macromolecule #33: 40S ribosomal protein S7
+Macromolecule #34: 40S ribosomal protein S8
+Macromolecule #35: KLLA0E23673p
+Macromolecule #36: KLLA0A10483p
+Macromolecule #37: KLLA0F18040p
+Macromolecule #38: 40S ribosomal protein S14
+Macromolecule #39: 40S ribosomal protein S21
+Macromolecule #40: 40S ribosomal protein S22
+Macromolecule #41: 40S ribosomal protein S24
+Macromolecule #42: RPS23
+Macromolecule #43: 40S ribosomal protein S26
+Macromolecule #44: 40S ribosomal protein S27
+Macromolecule #45: Eukaryotic translation initiation factor 3 subunit B
+Macromolecule #46: Eukaryotic translation initiation factor 3 subunit I
+Macromolecule #47: Eukaryotic translation initiation factor 3 subunit G
+Macromolecule #48: MAGNESIUM ION
+Macromolecule #49: ZINC ION
+Macromolecule #50: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
+Macromolecule #51: METHIONINE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.18 mg/mL | ||||||||||||||
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Buffer | pH: 6.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 90.0 K / Max: 100.0 K |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 3 / Number real images: 5500 / Average exposure time: 1.1 sec. / Average electron dose: 32.0 e/Å2 Details: Images were collected in movie-mode at 32 frames per second |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 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
Refinement | Space: RECIPROCAL / Protocol: OTHER / Target criteria: FSC |
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Output model | ![]() PDB-6gsn: |