+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2198 | |||||||||
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Title | Architecture of human translation initiation factor 3 | |||||||||
Map data | reconstruction using Maximum-likelihood | |||||||||
Sample |
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Keywords | translation initiation / eukaryotic initiation factor 3 / ribosome / proteasome / PCI-MPN domains | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 20.0 Å | |||||||||
Authors | Querol-Audi J / Sun C / Mortimer S / Arias-Palomo E / Vogan J / Doudna J / Nogales E / Cate J | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2013 Title: Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation. Authors: Chaomin Sun / Jordi Querol-Audí / Stefanie A Mortimer / Ernesto Arias-Palomo / Jennifer A Doudna / Eva Nogales / Jamie H D Cate / Abstract: The initiation of protein synthesis plays an essential regulatory role in human biology. At the center of the initiation pathway, the 13-subunit eukaryotic translation initiation factor 3 (eIF3) ...The initiation of protein synthesis plays an essential regulatory role in human biology. At the center of the initiation pathway, the 13-subunit eukaryotic translation initiation factor 3 (eIF3) controls access of other initiation factors and mRNA to the ribosome by unknown mechanisms. Using electron microscopy (EM), bioinformatics and biochemical experiments, we identify two highly conserved RNA-binding motifs in eIF3 that direct translation initiation from the hepatitis C virus internal ribosome entry site (HCV IRES) RNA. Mutations in the RNA-binding motif of subunit eIF3a weaken eIF3 binding to the HCV IRES and the 40S ribosomal subunit, thereby suppressing eIF2-dependent recognition of the start codon. Mutations in the eIF3c RNA-binding motif also reduce 40S ribosomal subunit binding to eIF3, and inhibit eIF5B-dependent steps downstream of start codon recognition. These results provide the first connection between the structure of the central translation initiation factor eIF3 and recognition of the HCV genomic RNA start codon, molecular interactions that likely extend to the human transcriptome. | |||||||||
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_2198.map.gz | 1.3 MB | EMDB map data format | |
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Header (meta data) | emd-2198-v30.xml emd-2198.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | 2198_emd_2198.png | 106.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2198 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2198 | HTTPS FTP |
-Validation report
Summary document | emd_2198_validation.pdf.gz | 209.8 KB | Display | EMDB validaton report |
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Full document | emd_2198_full_validation.pdf.gz | 209 KB | Display | |
Data in XML | emd_2198_validation.xml.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2198 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2198 | HTTPS FTP |
-Related 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_2198.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | reconstruction using Maximum-likelihood | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.67 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 : PCI MPN core of the human eukaryotic translation initiation facto...
Entire | Name: PCI MPN core of the human eukaryotic translation initiation factor eIF3 |
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Components |
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-Supramolecule #1000: PCI MPN core of the human eukaryotic translation initiation facto...
Supramolecule | Name: PCI MPN core of the human eukaryotic translation initiation factor eIF3 type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Subcomplex containing 8 core subunits / Number unique components: 8 |
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Molecular weight | Theoretical: 400 KDa |
-Macromolecule #1: eIF3 a
Macromolecule | Name: eIF3 a / type: protein_or_peptide / ID: 1 / Details: truncated version, contains residues 5-654 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #2: eIF3 c
Macromolecule | Name: eIF3 c / type: protein_or_peptide / ID: 2 / Details: truncated version, contains residues 302-913 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #3: eIF3 e
Macromolecule | Name: eIF3 e / type: protein_or_peptide / ID: 3 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #4: eIF3 f
Macromolecule | Name: eIF3 f / type: protein_or_peptide / ID: 4 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #5: eIF3 h
Macromolecule | Name: eIF3 h / type: protein_or_peptide / ID: 5 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #6: eIF3 k
Macromolecule | Name: eIF3 k / type: protein_or_peptide / ID: 6 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #7: eIF3 l
Macromolecule | Name: eIF3 l / type: protein_or_peptide / ID: 7 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #8: eIF3 m
Macromolecule | Name: eIF3 m / type: protein_or_peptide / ID: 8 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 Details: 20mM Hepes, 75mM KCl, 0.5mM EDTA, 1mM DTT, 2mM MgCl2, 3% trehalose |
Staining | Type: NEGATIVE / Details: vitrified |
Grid | Details: C-flat plasma cleaned with Solarus |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Oct 9, 2011 |
Image recording | Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | automatic particle selection with template correlator |
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CTF correction | Details: each image |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Software - Name: ML3D / Number images used: 32227 |