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Yorodumi- PDB-4px9: DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop -
+Open data
-Basic information
Entry | Database: PDB / ID: 4px9 | ||||||
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Title | DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop | ||||||
Components | ATP-dependent RNA helicase DDX3X | ||||||
Keywords | TRANSLATION / RNA BINDING PROTEIN / DEAD-box helicase / HYDROLASE | ||||||
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 / RNA stem-loop binding / cell leading edge / lipid homeostasis / positive regulation of interferon-alpha production / positive regulation of translational initiation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / ribosomal small subunit binding / transcription factor binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of type I interferon production / positive regulation of G1/S transition of mitotic cell cycle / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / negative regulation of intrinsic apoptotic signaling pathway / signaling adaptor activity / translation initiation factor binding / stress granule assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of protein autophosphorylation / translational initiation / DNA helicase activity / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / protein serine/threonine kinase activator activity / intrinsic apoptotic signaling pathway / positive regulation of translation / cytosolic ribosome assembly / chromosome segregation / response to virus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein serine/threonine kinase activity / mRNA 5'-UTR binding / negative regulation of cell growth / cellular response to virus / Wnt signaling pathway / 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 / cell differentiation / negative regulation of translation / RNA helicase activity / RNA helicase / intracellular signal transduction / cadherin binding / positive regulation of apoptotic process / mRNA binding / innate immune response / GTPase activity / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Epling, L.B. / Grace, C.R. / Lowe, B.R. / Partridge, J.F. / Enemark, E.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Cancer-Associated Mutants of RNA Helicase DDX3X Are Defective in RNA-Stimulated ATP Hydrolysis. Authors: Epling, L.B. / Grace, C.R. / Lowe, B.R. / Partridge, J.F. / Enemark, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4px9.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4px9.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 4px9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/4px9 ftp://data.pdbj.org/pub/pdb/validation_reports/px/4px9 | HTTPS FTP |
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-Related structure data
Related structure data | 4pxaC 2i4iS C: citing same article (ref.) 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 33021.934 Da / Num. of mol.: 3 / Fragment: UNP residues 135-407 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DBX, DDX3, DDX3X / Plasmid: pLE231 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: O00571, RNA helicase #2: Chemical | |
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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: 2.02 Å3/Da / Density % sol: 39.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 50 mM Hepes 7.6; 7% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 28, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 34297 / Num. obs: 34163 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 26.95 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.28 / Num. unique all: 3458 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2I4I Resolution: 2.31→36.11 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1794086.67 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.1571 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.31→36.11 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.31→2.38 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
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Xplor file |
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