+Open data
-Basic information
Entry | Database: PDB / ID: 2vso | ||||||
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Title | Crystal Structure of a Translation Initiation Complex | ||||||
Components |
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Keywords | HYDROLASE/TRANSLATION / ACETYLATION / ATP-BINDING / PHOSPHOPROTEIN / PROTEIN BIOSYNTHESIS / TRANSLATION REGULATION / TRANSLATION INITIATION / INITIATION FACTOR / NUCLEOTIDE-BINDING / HELICASE / HYDROLASE / CYTOPLASM / RNA-BINDING / HYDROLASE-TRANSLATION complex | ||||||
Function / homology | Function and homology information Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / Deadenylation of mRNA / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / regulation of protein metabolic process / positive regulation of endoplasmic reticulum unfolded protein response / ATP-dependent activity, acting on RNA / mTORC1-mediated signalling / regulation of translational initiation ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / Deadenylation of mRNA / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / regulation of protein metabolic process / positive regulation of endoplasmic reticulum unfolded protein response / ATP-dependent activity, acting on RNA / mTORC1-mediated signalling / regulation of translational initiation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / cellular response to glucose starvation / stress granule assembly / translation initiation factor activity / ribosomal large subunit biogenesis / translational initiation / molecular condensate scaffold activity / P-body / cytoplasmic stress granule / RNA helicase activity / RNA helicase / ribosome / mRNA binding / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Schutz, P. / Bumann, M. / Oberholzer, A.E. / Bieniossek, C. / Altmann, M. / Trachsel, H. / Baumann, U. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Crystal Structure of the Yeast Eif4A-Eif4G Complex: An RNA-Helicase Controlled by Protein-Protein Interactions. Authors: Schutz, P. / Bumann, M. / Oberholzer, A.E. / Bieniossek, C. / Trachsel, H. / Altmann, M. / Baumann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vso.cif.gz | 495.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vso.ent.gz | 407.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vso_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2vso_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2vso_validation.xml.gz | 45.9 KB | Display | |
Data in CIF | 2vso_validation.cif.gz | 62.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/2vso ftp://data.pdbj.org/pub/pdb/validation_reports/vs/2vso | HTTPS FTP |
-Related structure data
Related structure data | 2vsxC 1fukS 1hu3S 1qdeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 44745.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PET-28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA References: UniProt: P10081, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #2: Protein | Mass: 32360.195 Da / Num. of mol.: 2 / Fragment: MIDDLE DOMAIN, 4A-BINDING, 572-854 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PET-28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39935 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.2 M TARTRATE, 20% PEG3350, PH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 1, 2006 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 48104 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 37.35 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.6→2.75 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.5 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1QDE, 1FUK, 1HU3 Resolution: 2.6→48.012 Å / SU ML: 0.4 / σ(F): 2 / Phase error: 29.17 / Stereochemistry target values: ML Details: DISORDERED SIDE CHAINS WERE FREQUENTLY MODELED AS ALANINE.
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.328 Å2 / ksol: 0.362 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→48.012 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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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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