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- EMDB-3049: Structure of a partial yeast 48S preinitiation complex in open co... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3049 | |||||||||
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Title | Structure of a partial yeast 48S preinitiation complex in open conformation | |||||||||
![]() | To see a continuous density for factor eIF3 at the 40S subunit interface, apply a Gaussian filtering of 1.8 and a contour level of 0.018. | |||||||||
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![]() | Eukaryotic translation initiation / 48S / 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 / translational termination / 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 / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||
![]() | Llacer JL / Hussain T / Ramakrishnan V | |||||||||
![]() | ![]() 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
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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) | ![]() ![]() | 17 KB 17 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() ![]() | 359.6 KB 359.6 KB | ||
Others | ![]() ![]() | 80.9 MB 80.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gsmM ![]() 3047C ![]() 3048C ![]() 3050C ![]() 3jamC ![]() 3japC ![]() 3jaq C: citing same article ( M: atomic model generated by this map |
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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 | To see a continuous density for factor eIF3 at the 40S subunit interface, apply a Gaussian filtering of 1.8 and a contour level of 0.018. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Supplemental map: emd 3049 half map 1.map
File | emd_3049_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 3049 half map 2.map
File | emd_3049_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Partial yeast 48S preinitiation complex in open conformation
Entire | Name: Partial yeast 48S preinitiation complex in open conformation |
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Components |
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-Supramolecule #1000: Partial yeast 48S preinitiation complex in open conformation
Supramolecule | Name: Partial yeast 48S preinitiation complex in open conformation type: sample / ID: 1000 / Oligomeric state: 1 / Number unique components: 7 |
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Molecular weight | Theoretical: 1.75 MDa |
-Supramolecule #1: Ribosome small subunit
Supramolecule | Name: Ribosome small subunit / type: complex / ID: 1 / Name.synonym: 40S / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S, SSU RNA 18S |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.2 MDa |
-Macromolecule #1: Eukaryotic initiation factor 1
Macromolecule | Name: Eukaryotic initiation factor 1 / type: protein_or_peptide / ID: 1 / Name.synonym: eIF1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 12.3 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Eukaryotic translation initiation factor eIF-1 |
-Macromolecule #2: Eukaryotic initiation factor 1A
Macromolecule | Name: Eukaryotic initiation factor 1A / type: protein_or_peptide / ID: 2 / Name.synonym: eIF1A / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 17.4 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Eukaryotic translation initiation factor 1A |
-Macromolecule #3: Eukaryotic initiation factor 2
Macromolecule | Name: Eukaryotic initiation factor 2 / type: protein_or_peptide / ID: 3 / Name.synonym: eIF2 Details: Uniprot codes are: alpha-P20459 beta-P09064 gamma-P32481 Number of copies: 1 / Oligomeric state: Three subunits, alpha, beta, gamma / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 124 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #4: Eukaryotic initiation factor 3
Macromolecule | Name: Eukaryotic initiation factor 3 / type: protein_or_peptide / ID: 4 / Name.synonym: eIF3 Details: Uniprot codes are: 3a-P38249, 3b-P06103, 3c-P32497, 3g-A6ZZ25, 3i-P40217 Number of copies: 1 / Oligomeric state: Five subunits, 3a, 3b, 3c, 3g, 3i / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 395 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #5: Initiator transfer RNA
Macromolecule | Name: Initiator transfer RNA / type: rna / ID: 5 / Name.synonym: Met-tRNAi / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23 KDa |
Sequence | String: AGCGCCGUGG CGCAGUGGAA GCGCGCAGGG CUCAUAACCC UGAUGUCCUC GGAUCGAAAC CGAGCGGCGC UACCA |
-Macromolecule #6: Messenger RNA
Macromolecule | Name: Messenger RNA / type: rna / ID: 6 / Name.synonym: mRNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 7.33 KDa |
Sequence | String: GGAAUCUCUC UCUAUCCUCU CUCUC |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.17 mg/mL |
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Buffer | pH: 6.5 Details: 20mM MES-KOH, 40mM K-acetate, 10mM NH4-acetate, 8mM Mg-acetate, 2mM DTT |
Grid | Details: Quantifoil R2/2 400 mesh copper grids with 4-5 nm thin carbon on top |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Timed resolved state: 30 second incubation time / Method: Blot for 2.5-3 seconds before plunging |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification |
Details | Complete dataset was collected in 2 non-consecutive sessions |
Date | Apr 28, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 2056 / Average electron dose: 27 e/Å2 Details: Complete dataset was collected in 2 non-consecutive sessions |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 78000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: 2 |
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Software | Name: Chimera, Coot, Refmac |
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: R-factor, FSC |
Output model | ![]() PDB-6gsm: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: K |
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Software | Name: Chimera, Coot, Refmac |
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: R-factor, FSC |
Output model | ![]() PDB-6gsm: |