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- PDB-3ns6: Crystal structure of hte RNA recognition motif of yeast eIF3b res... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ns6 | ||||||
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Title | Crystal structure of hte RNA recognition motif of yeast eIF3b residues 76-170 | ||||||
![]() | Eukaryotic translation initiation factor 3 subunit B | ||||||
![]() | TRANSLATION | ||||||
Function / homology | ![]() multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / formation of cytoplasmic translation initiation 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 ...multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / formation of cytoplasmic translation initiation 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 binding / translational initiation / translation initiation factor activity / cytoplasmic stress granule / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Khoshnevis, S. / Neumann, P. / Ficner, R. | ||||||
![]() | ![]() Title: Crystal structure of the RNA recognition motif of yeast translation initiation factor eIF3b reveals differences to human eIF3b. Authors: Khoshnevis, S. / Neumann, P. / Ficner, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.8 KB | Display | ![]() |
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PDB format | ![]() | 80.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439 KB | Display | ![]() |
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Full document | ![]() | 440.2 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ns5C ![]() 3sxlS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11079.933 Da / Num. of mol.: 2 / Fragment: residues 76-170 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CDC63, PRT1, YOR361C / Plasmid: pGEX-6P-1 / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.49 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8 Details: 30% PEG4000, 200 mM Li2SO4 and 100 mM Hepes pH 8. The crystals were grown in a sitting drop at 20 degrees by mixing 1uL of protein (11 mg/mL) with 1uL of reservoir, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→38.026 Å / Num. obs: 48971 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.437 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.42 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SXL Resolution: 1.25→38.026 Å / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.9161 / SU ML: 0.11 / σ(F): 1.36 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.565 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 42.61 Å2 / Biso mean: 13.5729 Å2 / Biso min: 4.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→38.026 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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