+Open data
-Basic information
Entry | Database: PDB / ID: 7ymf | ||||||
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Title | Crystal Structure of DDX3X449_450ET>DP | ||||||
Components | (ATP-dependent RNA helicase DDX3X) x 2 | ||||||
Keywords | HYDROLASE / DDX3X / NUCLEAR PROTEIN | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Xiong, J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of DDX3X449_450ET>DP Authors: Xiong, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ymf.cif.gz | 110 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ymf.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ymf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/7ymf ftp://data.pdbj.org/pub/pdb/validation_reports/ym/7ymf | HTTPS FTP |
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-Related structure data
Related structure data | 4pxaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34187.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX3X / Production host: Escherichia coli (E. coli) / References: UniProt: O00571, RNA helicase |
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#2: Protein | Mass: 20255.672 Da / Num. of mol.: 1 / Mutation: E449D, T450P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX3X / Production host: Escherichia coli (E. coli) / References: UniProt: O00571, RNA helicase |
#3: 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: 2.34 Å3/Da / Density % sol: 47.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES pH 6.5, 1.5 M Sodium Formate , 50 mM Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 21930 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 27.52 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.039 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 2050 / CC1/2: 0.92 / Rpim(I) all: 0.264 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PXA Resolution: 2.3→49.32 Å / SU ML: 0.2455 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 25.378 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: 34.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49.32 Å
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Refine LS restraints |
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LS refinement shell |
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