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Yorodumi- PDB-6l5n: Crystal structure of human DEAD-box RNA helicase DDX21 at post-un... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l5n | ||||||
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Title | Crystal structure of human DEAD-box RNA helicase DDX21 at post-unwound state | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / RNA bound post-unwound state / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information RNA polymerase inhibitor activity / 7SK snRNA binding / R-loop processing / central nervous system projection neuron axonogenesis / positive regulation of myeloid dendritic cell cytokine production / B-WICH complex / miRNA binding / positive regulation of transcription by RNA polymerase III / negative regulation of transcription by RNA polymerase I / snoRNA binding ...RNA polymerase inhibitor activity / 7SK snRNA binding / R-loop processing / central nervous system projection neuron axonogenesis / positive regulation of myeloid dendritic cell cytokine production / B-WICH complex / miRNA binding / positive regulation of transcription by RNA polymerase III / negative regulation of transcription by RNA polymerase I / snoRNA binding / positive regulation of transcription by RNA polymerase I / response to exogenous dsRNA / Major pathway of rRNA processing in the nucleolus and cytosol / neuron projection maintenance / B-WICH complex positively regulates rRNA expression / microtubule cytoskeleton organization / osteoblast differentiation / rRNA processing / double-stranded RNA binding / chromosome / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / transcription by RNA polymerase II / RNA helicase activity / rRNA binding / RNA helicase / chromatin remodeling / innate immune response / mRNA binding / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.242 Å | ||||||
Authors | Chen, Z.J. / Hu, X.J. / Zhou, Z. / Li, J.X. | ||||||
Citation | Journal: Adv Sci / Year: 2020 Title: Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. Authors: Chen, Z. / Li, Z. / Hu, X. / Xie, F. / Kuang, S. / Zhan, B. / Gao, W. / Chen, X. / Gao, S. / Li, Y. / Wang, Y. / Qian, F. / Ding, C. / Gan, J. / Ji, C. / Xu, X. / Zhou, Z. / Huang, J. / He, H.H. / Li, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l5n.cif.gz | 170 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l5n.ent.gz | 139.2 KB | Display | PDB format |
PDBx/mmJSON format | 6l5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/6l5n ftp://data.pdbj.org/pub/pdb/validation_reports/l5/6l5n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42471.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR30, RNA helicase #2: RNA chain | Mass: 4547.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #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: 2.6 Å3/Da / Density % sol: 52.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 7% MPD and 0.1M Bicine, pH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 11, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97849 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.242→71.867 Å / Num. obs: 43794 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.111 / Rsym value: 0.091 / Net I/av σ(I): 6.2 / Net I/σ(I): 11.6 / Num. measured all: 276183 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.242→33.52 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.71 / 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: 117.35 Å2 / Biso mean: 37.7253 Å2 / Biso min: 7.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.242→33.52 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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