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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11439 | |||||||||
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Title | Structure of a yeast ABCE1-bound 48S initiation complex | |||||||||
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![]() | Translation / Initiation / Ribosome Recycling / ABC Proteins / RIBOSOME | |||||||||
Function / homology | ![]() formation of translation initiation ternary complex / eukaryotic initiation factor eIF2 binding / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / incipient cellular bud site / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex ...formation of translation initiation ternary complex / eukaryotic initiation factor eIF2 binding / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / incipient cellular bud site / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / ribosome disassembly / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / regulation of translational initiation / nonfunctional rRNA decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of cellular amino acid metabolic process / ribosomal small subunit binding / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / positive regulation of protein kinase activity / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small subunit export from nucleus / 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) / negative regulation of translational initiation / DNA-(apurinic or apyrimidinic site) endonuclease activity / translation initiation factor binding / translation initiation factor activity / cellular response to amino acid starvation / rescue of stalled ribosome / GTPase activator activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / positive regulation of translation / 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 biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / iron ion binding / G protein-coupled receptor signaling pathway / negative regulation of gene expression / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / protein kinase binding / ATP hydrolysis activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.2 Å | |||||||||
![]() | Kratzat H / Mackens-Kiani T | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes. Authors: Hanna Kratzat / Timur Mackens-Kiani / Michael Ameismeier / Mia Potocnjak / Jingdong Cheng / Estelle Dacheux / Abdelkader Namane / Otto Berninghausen / Franz Herzog / Micheline Fromont-Racine ...Authors: Hanna Kratzat / Timur Mackens-Kiani / Michael Ameismeier / Mia Potocnjak / Jingdong Cheng / Estelle Dacheux / Abdelkader Namane / Otto Berninghausen / Franz Herzog / Micheline Fromont-Racine / Thomas Becker / Roland Beckmann / ![]() ![]() Abstract: In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub-complexes. ...In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub-complexes. These comprise/include the large eIF3 complex, eIF3j (Hcr1 in yeast) and the ATP-binding cassette protein ABCE1 (Rli1 in yeast). The ATPase is mainly active as a recycling factor, but it can remain bound to the dissociated 40S subunit until formation of the next 43S pre-initiation complexes. However, its functional role and native architectural context remains largely enigmatic. Here, we present an architectural inventory of native yeast and human ABCE1-containing pre-initiation complexes by cryo-EM. We found that ABCE1 was mostly associated with early 43S, but also with later 48S phases of initiation. It adopted a novel hybrid conformation of its nucleotide-binding domains, while interacting with the N-terminus of eIF3j. Further, eIF3j occupied the mRNA entry channel via its ultimate C-terminus providing a structural explanation for its antagonistic role with respect to mRNA binding. Overall, the native human samples provide a near-complete molecular picture of the architecture and sophisticated interaction network of the 43S-bound eIF3 complex and the eIF2 ternary complex containing the initiator tRNA. | |||||||||
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 | ![]() | 140.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 66 KB 66 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.9 KB | Display | ![]() |
Images | ![]() | 58.1 KB | ||
Filedesc metadata | ![]() | 14.5 KB | ||
Others | ![]() ![]() | 141.1 MB 140.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1012.5 KB | Display | ![]() |
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Full document | ![]() | 1012.1 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zu9MC ![]() 6zceC ![]() 6zvjC ![]() 7a09C ![]() 7a1gC 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
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Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_11439_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11439_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : ABCE1-bound 48S initiation complex
+Supramolecule #1: ABCE1-bound 48S initiation complex
+Macromolecule #1: 18S ribosomal RNA
+Macromolecule #37: tRNA
+Macromolecule #42: mRNA
+Macromolecule #2: 40S ribosomal protein S0-A
+Macromolecule #3: 40S ribosomal protein S1-A
+Macromolecule #4: 40S ribosomal protein S2
+Macromolecule #5: 40S ribosomal protein S4-A
+Macromolecule #6: 40S ribosomal protein S6-A
+Macromolecule #7: 40S ribosomal protein S7-A
+Macromolecule #8: 40S ribosomal protein S8-A
+Macromolecule #9: 40S ribosomal protein S9-A
+Macromolecule #10: 40S ribosomal protein S11-A
+Macromolecule #11: 40S ribosomal protein S13
+Macromolecule #12: 40S ribosomal protein S14-A
+Macromolecule #13: 40S ribosomal protein S21-A
+Macromolecule #14: 40S ribosomal protein S22-A
+Macromolecule #15: 40S ribosomal protein S23-A
+Macromolecule #16: 40S ribosomal protein S24-A
+Macromolecule #17: 40S ribosomal protein S26-A
+Macromolecule #18: 40S ribosomal protein S27-A
+Macromolecule #19: 40S ribosomal protein S30-A
+Macromolecule #20: 40S ribosomal protein S15
+Macromolecule #21: 40S ribosomal protein S3
+Macromolecule #22: Rps5p
+Macromolecule #23: 40S ribosomal protein S10-A
+Macromolecule #24: 40S ribosomal protein S12
+Macromolecule #25: 40S ribosomal protein S16-A
+Macromolecule #26: 40S ribosomal protein S17-A
+Macromolecule #27: 40S ribosomal protein S18-A
+Macromolecule #28: 40S ribosomal protein S19-A
+Macromolecule #29: 40S ribosomal protein S20
+Macromolecule #30: 40S ribosomal protein S25-A
+Macromolecule #31: 40S ribosomal protein S29-A
+Macromolecule #32: Ubiquitin-40S ribosomal protein S31
+Macromolecule #33: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #34: 40S ribosomal protein S28-B
+Macromolecule #35: Eukaryotic translation initiation factor 3 subunit I
+Macromolecule #36: Eukaryotic translation initiation factor 3 subunit G
+Macromolecule #38: Eukaryotic translation initiation factor 5
+Macromolecule #39: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #40: Eukaryotic translation initiation factor 3 subunit B
+Macromolecule #41: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #43: Eukaryotic translation initiation factor 1A
+Macromolecule #44: Translation initiation factor RLI1
+Macromolecule #45: MAGNESIUM ION
+Macromolecule #46: ZINC ION
+Macromolecule #47: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #48: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #49: IRON/SULFUR CLUSTER
-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 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |