[English] 日本語
Yorodumi- PDB-6l5m: Crystal structure of human DEAD-box RNA helicase DDX21 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l5m | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human DEAD-box RNA helicase DDX21 in complex with AMP | ||||||
Components | Nucleolar RNA helicase 2 | ||||||
Keywords | RNA BINDING PROTEIN / with AMP | ||||||
Function / homology | Function and homology information RNA polymerase inhibitor activity / 7SK snRNA binding / R-loop processing / positive regulation of myeloid dendritic cell cytokine production / B-WICH complex / miRNA binding / negative regulation of transcription by RNA polymerase I / positive regulation of transcription by RNA polymerase III / snoRNA binding / positive regulation of transcription by RNA polymerase I ...RNA polymerase inhibitor activity / 7SK snRNA binding / R-loop processing / positive regulation of myeloid dendritic cell cytokine production / B-WICH complex / miRNA binding / negative regulation of transcription by RNA polymerase I / positive regulation of transcription by RNA polymerase III / snoRNA binding / positive regulation of transcription by RNA polymerase I / response to exogenous dsRNA / Major pathway of rRNA processing in the nucleolus and cytosol / B-WICH complex positively regulates rRNA expression / osteoblast differentiation / rRNA processing / double-stranded RNA binding / chromosome / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / transcription by RNA polymerase II / RNA helicase activity / rRNA binding / RNA helicase / chromatin remodeling / innate immune response / mRNA binding / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6l5m.cif.gz | 363.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6l5m.ent.gz | 295.9 KB | Display | PDB format |
PDBx/mmJSON format | 6l5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l5m_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6l5m_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6l5m_validation.xml.gz | 60.8 KB | Display | |
Data in CIF | 6l5m_validation.cif.gz | 82.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/6l5m ftp://data.pdbj.org/pub/pdb/validation_reports/l5/6l5m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42283.492 Da / Num. of mol.: 5 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: Chemical | ChemComp-AMP / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.79 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 19% pEG3350, 0.18M ammonium citrate, 40mM myo-inositol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→126.378 Å / Num. obs: 51933 / % possible obs: 95.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 30.36 Å2 / Rsym value: 0.209 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 51933 / Rsym value: 0.682 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.7→36.51 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.846 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.356
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.48 Å2 / Biso mean: 25.7 Å2 / Biso min: 3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→36.51 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
|