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Yorodumi- PDB-8ssw: Crystal structure of DEAD-box RNA helicase DDX3X in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 8ssw | ||||||
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Title | Crystal structure of DEAD-box RNA helicase DDX3X in complex with ADP at pre-unwound state | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / DEAD-box RNA helicase / DDX3X / pre-unwound state / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information positive regulation of protein acetylation / CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / RNA secondary structure unwinding ...positive regulation of protein acetylation / CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / RNA secondary structure unwinding / gamete generation / NLRP3 inflammasome complex / positive regulation of protein K63-linked ubiquitination / cellular response to arsenic-containing substance / poly(A) binding / gamma-tubulin binding / cellular response to osmotic stress / P granule / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of NLRP3 inflammasome complex assembly / cell leading edge / lipid homeostasis / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / transcription factor binding / ribosomal small subunit binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of interferon-alpha production / positive regulation of type I interferon production / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of translational initiation / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / signaling adaptor activity / negative regulation of intrinsic apoptotic signaling pathway / stress granule assembly / RNA stem-loop binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of protein autophosphorylation / translational initiation / translation initiation factor binding / DNA helicase activity / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / protein serine/threonine kinase activator activity / intrinsic apoptotic signaling pathway / cytosolic ribosome assembly / chromosome segregation / positive regulation of translation / response to virus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein serine/threonine kinase activity / negative regulation of cell growth / cellular response to virus / Wnt signaling pathway / mRNA 5'-UTR binding / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / lamellipodium / positive regulation of cell growth / secretory granule lumen / ficolin-1-rich granule lumen / RNA helicase activity / negative regulation of translation / cell differentiation / intracellular signal transduction / RNA helicase / cadherin binding / positive regulation of apoptotic process / negative regulation of gene expression / innate immune response / GTPase activity / mRNA binding / centrosome / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Song, H. / Ji, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal structure of DEAD-box RNA helicase DDX3X in complex with ADP at pre-unwound state Authors: Song, H. / Ji, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ssw.cif.gz | 222.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ssw.ent.gz | 170.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ssw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/8ssw ftp://data.pdbj.org/pub/pdb/validation_reports/ss/8ssw | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / RNA chain , 2 types, 4 molecules ABCD
#1: Protein | Mass: 53701.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX3X, DBX, DDX3 / Production host: Escherichia coli (E. coli) / References: UniProt: O00571, RNA helicase #2: RNA chain | Mass: 9010.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 243 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.32 Å3/Da / Density % sol: 46.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG3350, Magnesium Chloride, etc. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2017 / Details: Si(111) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→40 Å / Num. obs: 42842 / % possible obs: 97.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.067 / Χ2: 1.037 / Net I/av σ(I): 11.2 / Net I/σ(I): 6.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→39.75 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 30.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→39.75 Å
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Refine LS restraints |
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LS refinement shell |
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