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Yorodumi- EMDB-3056: Structure of mammalian eIF3 in the context of the 43S preinitiati... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3056 | |||||||||
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Title | Structure of mammalian eIF3 in the context of the 43S preinitiation complex | |||||||||
Map data | Reconstruction of eIF3 octamer core | |||||||||
Sample |
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Keywords | eIF3 / eukaryotic Initiation Factor 3 / preinitiation complex / PCI/MPN core / eIF3g/i/b / eIF3d | |||||||||
Function / homology | Function and homology information viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / protein deubiquitination / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation initiation factor binding / translation initiation factor activity / positive regulation of translation / PML body / fibrillar center / metallopeptidase activity / ribosome binding / cysteine-type deubiquitinase activity / postsynaptic density / mRNA binding / synapse / nucleolus / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||
Authors | des-Georges A / Dhote V / Kuhn L / Hellen CUT / Pestova TV / Frank J / Hashem Y | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Structure of mammalian eIF3 in the context of the 43S preinitiation complex. Authors: Amedee des Georges / Vidya Dhote / Lauriane Kuhn / Christopher U T Hellen / Tatyana V Pestova / Joachim Frank / Yaser Hashem / Abstract: During eukaryotic translation initiation, 43S complexes, comprising a 40S ribosomal subunit, initiator transfer RNA and initiation factors (eIF) 2, 3, 1 and 1A, attach to the 5'-terminal region of ...During eukaryotic translation initiation, 43S complexes, comprising a 40S ribosomal subunit, initiator transfer RNA and initiation factors (eIF) 2, 3, 1 and 1A, attach to the 5'-terminal region of messenger RNA and scan along it to the initiation codon. Scanning on structured mRNAs also requires the DExH-box protein DHX29. Mammalian eIF3 contains 13 subunits and participates in nearly all steps of translation initiation. Eight subunits having PCI (proteasome, COP9 signalosome, eIF3) or MPN (Mpr1, Pad1, amino-terminal) domains constitute the structural core of eIF3, to which five peripheral subunits are flexibly linked. Here we present a cryo-electron microscopy structure of eIF3 in the context of the DHX29-bound 43S complex, showing the PCI/MPN core at ∼6 Å resolution. It reveals the organization of the individual subunits and their interactions with components of the 43S complex. We were able to build near-complete polyalanine-level models of the eIF3 PCI/MPN core and of two peripheral subunits. The implications for understanding mRNA ribosomal attachment and scanning are discussed. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3056.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-3056-v30.xml emd-3056.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | 13501.jpg | 105.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3056 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3056 | HTTPS FTP |
-Validation report
Summary document | emd_3056_validation.pdf.gz | 209.6 KB | Display | EMDB validaton report |
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Full document | emd_3056_full_validation.pdf.gz | 208.7 KB | Display | |
Data in XML | emd_3056_validation.xml.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3056 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3056 | HTTPS FTP |
-Related structure data
Related structure data | 5a5tMC 3057C 3058C 5a5uC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3056.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of eIF3 octamer core | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.66 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : eIF3 octamer core of Rabbit eIF3
Entire | Name: eIF3 octamer core of Rabbit eIF3 |
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Components |
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-Supramolecule #1000: eIF3 octamer core of Rabbit eIF3
Supramolecule | Name: eIF3 octamer core of Rabbit eIF3 / type: sample / ID: 1000 Details: The sample was monodisperse, eIF3 octamer core was locally refined from a reconstruction of the mammalian 43S preinitiation complex Oligomeric state: One octamer / Number unique components: 7 |
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Molecular weight | Experimental: 450 KDa / Theoretical: 450 KDa |
-Supramolecule #1: 40S small ribosomal subunit
Supramolecule | Name: 40S small ribosomal subunit / type: complex / ID: 1 / Name.synonym: SSU / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: Cytoplasm |
-Macromolecule #1: eukaryotic initiation factor 3
Macromolecule | Name: eukaryotic initiation factor 3 / type: protein_or_peptide / ID: 1 / Name.synonym: eIF3 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: Cytoplasm |
-Macromolecule #2: eukaryotic initiation factor 2
Macromolecule | Name: eukaryotic initiation factor 2 / type: protein_or_peptide / ID: 2 / Name.synonym: eIF2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: Cytoplasm |
-Macromolecule #4: DHX29
Macromolecule | Name: DHX29 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: Cytoplasm |
-Macromolecule #5: eukaryotic initiation factor 1
Macromolecule | Name: eukaryotic initiation factor 1 / type: protein_or_peptide / ID: 5 / Name.synonym: eIF1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: Cytoplasm |
-Macromolecule #6: eukaryotic initiation factor 1A
Macromolecule | Name: eukaryotic initiation factor 1A / type: protein_or_peptide / ID: 6 / Name.synonym: eIF3e / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: Cytoplasm |
-Macromolecule #3: initiator transfer RNA
Macromolecule | Name: initiator transfer RNA / type: rna / ID: 3 / Name.synonym: tRNAiMet / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV |
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-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 80 K / Max: 105 K / Average: 100 K |
Date | Nov 1, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 6.35 µm / Number real images: 8000 / Average electron dose: 25 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 30120 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: PHILIPS ROTATION HOLDER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 87192 |