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Yorodumi- PDB-5zbz: Crystal structure of the DEAD domain of Human eIF4A with sanguinarine -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zbz | ||||||||||||
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Title | Crystal structure of the DEAD domain of Human eIF4A with sanguinarine | ||||||||||||
Components | Eukaryotic initiation factor 4A-I | ||||||||||||
Keywords | HYDROLASE / eukaryotic translation initiation factor 4A / sanguinarine / inhibitor / TRANSLATION | ||||||||||||
Function / homology | Function and homology information Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / RNA cap binding / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Ribosomal scanning and start codon recognition / Translation initiation complex formation ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / RNA cap binding / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Ribosomal scanning and start codon recognition / Translation initiation complex formation / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / translational initiation / translation initiation factor activity / helicase activity / ISG15 antiviral mechanism / double-stranded RNA binding / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.30860259206 Å | ||||||||||||
Authors | Ding, Y. / Ding, L. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Cell Chem Biol / Year: 2019 Title: Targeting the N Terminus of eIF4AI for Inhibition of Its Catalytic Recycling. Authors: Jiang, C. / Tang, Y. / Ding, L. / Tan, R. / Li, X. / Lu, J. / Jiang, J. / Cui, Z. / Tang, Z. / Li, W. / Cao, Z. / Schneider-Poetsch, T. / Jiang, W. / Luo, C. / Ding, Y. / Liu, J. / Dang, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zbz.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zbz.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 5zbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/5zbz ftp://data.pdbj.org/pub/pdb/validation_reports/zb/5zbz | HTTPS FTP |
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-Related structure data
Related structure data | 2zu6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24926.096 Da / Num. of mol.: 1 / Fragment: DEAD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A1, DDX2A, EIF4A / Plasmid: pMBP (pMal-C2x derived) Details (production host): N terminal MBP and poly-His tag, TEV cleavage site Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P60842, RNA helicase |
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#2: Chemical | ChemComp-SAU / |
#3: Chemical | ChemComp-MLI / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium malonate |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979253 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979253 Å / Relative weight: 1 |
Reflection | Resolution: 1.309→36.49 Å / Num. obs: 53159 / % possible obs: 90.66 % / Redundancy: 2 % / Biso Wilson estimate: 18.1276228586 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.02669 / Rpim(I) all: 0.02669 / Rrim(I) all: 0.03775 / Net I/σ(I): 12.23 |
Reflection shell | Resolution: 1.309→1.355 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3181 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 5697 / CC1/2: 0.763 / Rpim(I) all: 0.3181 / Rrim(I) all: 0.4498 / % possible all: 97.52 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZU6 Resolution: 1.30860259206→36.4916112542 Å / SU ML: 0.147287544653 / Cross valid method: FREE R-VALUE / σ(F): 0.31589380531 / σ(I): 1996 / Phase error: 23.7075111376 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.529063773 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.30860259206→36.4916112542 Å
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Refine LS restraints |
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LS refinement shell |
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