+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2166 | |||||||||
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Title | Architecture of human translation initiation factor 3 | |||||||||
Map data | cryo-EM reconstruction of the eIF3 PCI-MPN core complex | |||||||||
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: 15.0 Å | |||||||||
Authors | Querol-Audi J / Sun C / Vogan J / Cate J / Nogales E | |||||||||
Citation | Journal: Structure / Year: 2013 Title: Architecture of human translation initiation factor 3. Authors: Jordi Querol-Audi / Chaomin Sun / Jacob M Vogan / M Duane Smith / Yu Gu / Jamie H D Cate / Eva Nogales / Abstract: Eukaryotic translation initiation factor 3 (eIF3) plays a central role in protein synthesis by organizing the formation of the 43S preinitiation complex. Using genetic tag visualization by electron ...Eukaryotic translation initiation factor 3 (eIF3) plays a central role in protein synthesis by organizing the formation of the 43S preinitiation complex. Using genetic tag visualization by electron microscopy, we reveal the molecular organization of ten human eIF3 subunits, including an octameric core. The structure of eIF3 bears a close resemblance to that of the proteasome lid, with a conserved spatial organization of eight core subunits containing PCI and MPN domains that coordinate functional interactions in both complexes. We further show that eIF3 subunits a and c interact with initiation factors eIF1 and eIF1A, which control the stringency of start codon selection. Finally, we find that subunit j, which modulates messenger RNA interactions with the small ribosomal subunit, makes multiple independent interactions with the eIF3 octameric core. These results highlight the conserved architecture of eIF3 and how it scaffolds key factors that control translation initiation in higher eukaryotes, including humans. | |||||||||
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_2166.map.gz | 9.8 MB | EMDB map data format | |
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Header (meta data) | emd-2166-v30.xml emd-2166.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
Images | eIF3_core.tif | 763.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2166 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2166 | HTTPS FTP |
-Validation report
Summary document | emd_2166_validation.pdf.gz | 199.1 KB | Display | EMDB validaton report |
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Full document | emd_2166_full_validation.pdf.gz | 198.3 KB | Display | |
Data in XML | emd_2166_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2166 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2166 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2166.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryo-EM reconstruction of the eIF3 PCI-MPN core complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.31 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 / Cell: n/atruncated version, contains residues 302-913 |
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 | Number real images: 2100 / 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: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 172533 |
Final two d classification | Number classes: 4000 |