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- PDB-7a1g: Structure of a crosslinked yeast ABCE1-bound 43S pre-initiation c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7a1g | |||||||||
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Title | Structure of a crosslinked yeast ABCE1-bound 43S pre-initiation complex | |||||||||
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![]() | RIBOSOME / Translation / Initiation / Ribosome Recycling / ABC Proteins | |||||||||
Function / homology | ![]() formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / 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 ...formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / 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 / nonfunctional rRNA decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / translation initiation factor activity / cellular response to amino acid starvation / rescue of stalled ribosome / 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) / 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 / 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 / ATP hydrolysis activity / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
![]() | Mackens-Kiani, T. / Kratzat, H. / Cheng, J. / Berninghausen, O. / Becker, T. / Beckmann, R. | |||||||||
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
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | 1.4 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 172.5 KB | Display | |
Data in CIF | ![]() | 291.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11608MC ![]() 6zceC ![]() 6zu9C ![]() 6zvjC ![]() 7a09C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 1 types, 1 molecules 2
#1: RNA chain | Mass: 570585.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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+40S ribosomal protein ... , 31 types, 31 molecules PQRSTUVWXYZabcdefgEABCDFHIJKLMh
-Protein , 4 types, 5 molecules NOzyx
#32: Protein | Mass: 8388.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P05759 | ||
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#33: Protein | Mass: 34151.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38011 | ||
#35: Protein | Mass: 29611.225 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q05775 #36: Protein | | Mass: 67714.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q03195 |
-Non-polymers , 4 types, 85 molecules ![](data/chem/img/MG.gif)
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#37: Chemical | ChemComp-MG / #38: Chemical | #39: Chemical | #40: Chemical | ChemComp-ADP / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: ABCE1-bound 43S PIC / Type: RIBOSOME / Entity ID: #1-#36 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 44.8 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25245 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.27 Å2 | ||||||||||||||||||||||||
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