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Yorodumi- PDB-4u1d: Structure of the PCI domain of translation initiation factor eIF3a -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u1d | ||||||
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Title | Structure of the PCI domain of translation initiation factor eIF3a | ||||||
Components | Eukaryotic translation initiation factor 3 subunit A | ||||||
Keywords | TRANSLATION / translation initiation / eIF3 complex / PCI domain | ||||||
Function / homology | Function and homology information 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 / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex ...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 / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor activity / translational initiation / cytoplasmic stress granule / mRNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å | ||||||
Authors | Erzberger, J.P. / Schaefer, T. / Ban, N. | ||||||
Citation | Journal: Cell / Year: 2014 Title: Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex. Authors: Jan P Erzberger / Florian Stengel / Riccardo Pellarin / Suyang Zhang / Tanja Schaefer / Christopher H S Aylett / Peter Cimermančič / Daniel Boehringer / Andrej Sali / Ruedi Aebersold / Nenad Ban / Abstract: Eukaryotic translation initiation requires the recruitment of the large, multiprotein eIF3 complex to the 40S ribosomal subunit. We present X-ray structures of all major components of the minimal, ...Eukaryotic translation initiation requires the recruitment of the large, multiprotein eIF3 complex to the 40S ribosomal subunit. We present X-ray structures of all major components of the minimal, six-subunit Saccharomyces cerevisiae eIF3 core. These structures, together with electron microscopy reconstructions, cross-linking coupled to mass spectrometry, and integrative structure modeling, allowed us to position and orient all eIF3 components on the 40S⋅eIF1 complex, revealing an extended, modular arrangement of eIF3 subunits. Yeast eIF3 engages 40S in a clamp-like manner, fully encircling 40S to position key initiation factors on opposite ends of the mRNA channel, providing a platform for the recruitment, assembly, and regulation of the translation initiation machinery. The structures of eIF3 components reported here also have implications for understanding the architecture of the mammalian 43S preinitiation complex and the complex of eIF3, 40S, and the hepatitis C internal ribosomal entry site RNA. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u1d.cif.gz | 551.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u1d.ent.gz | 466.3 KB | Display | PDB format |
PDBx/mmJSON format | 4u1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u1d_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
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Full document | 4u1d_full_validation.pdf.gz | 447.2 KB | Display | |
Data in XML | 4u1d_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 4u1d_validation.cif.gz | 61.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/4u1d ftp://data.pdbj.org/pub/pdb/validation_reports/u1/4u1d | HTTPS FTP |
-Related structure data
Related structure data | 2670C 2671C 3j8bC 3j8cC 4u1cC 4u1eC 4u1fC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 57012.719 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: RPG1, TIF32, YBR079C, YBR0734 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38249 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.1 Å3/Da / Density % sol: 75 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, KSCN, Bis-Tris-propane / PH range: 6.8-8.8 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.294→40 Å / Num. obs: 48944 / % possible obs: 94.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 112 Å2 / Net I/σ(I): 11.14 |
Reflection shell | Resolution: 3.294→3.5 Å / Mean I/σ(I) obs: 1.53 / % possible all: 92.6 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 3.3→39.568 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 22.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 118.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→39.568 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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