+Open data
-Basic information
Entry | Database: PDB / ID: 7liu | ||||||
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Title | DDX3X bound to ATP analog and remodeled RNA:DNA hybrid | ||||||
Components |
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Keywords | RNA-BINDING PROTEIN/DNA / RNA / DEAD-box helicase / RNA helicase / ATPase / RNA BINDING PROTEIN / RNA-BINDING PROTEIN-DNA / 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 / molecular replacement / Resolution: 3.001 Å | ||||||
Authors | Enemark, E.J. / Yu, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: DDX3X bound to ATP analog and remodeled RNA:DNA hybrid Authors: Enemark, E.J. / Yu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7liu.cif.gz | 205.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7liu.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 7liu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/7liu ftp://data.pdbj.org/pub/pdb/validation_reports/li/7liu | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 50817.770 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: DNA/RNA hybrid | Mass: 4395.755 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Sequence design is as published in Mallam et al, Nature 2012 (PDB 4DB4) Source: (synth.) synthetic construct (others) #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | 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: 4.91 Å3/Da / Density % sol: 74.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPEs pH 7.5, 16% PEG 3350, 0.1 M Li3Citrate, 0.1 M Na3Citrate, 2% benzamidine-HCl, 5 mM ADP-BeF3 |
-Data collection
Diffraction | Mean temperature: 200 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 9, 2016 |
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: 3→50 Å / Num. obs: 43593 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 85.2 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.121 / Rsym value: 0.113 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4265 / CC1/2: 0.641 / Rpim(I) all: 0.379 / Rrim(I) all: 0.964 / Rsym value: 0.882 / % possible all: 99.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PXA Resolution: 3.001→40.54 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.39 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 178.97 Å2 / Biso mean: 89.6588 Å2 / Biso min: 35.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.001→40.54 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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