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- PDB-3fe2: Human DEAD-BOX RNA helicase DDX5 (P68), conserved domain I in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fe2 | ||||||
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Title | Human DEAD-BOX RNA helicase DDX5 (P68), conserved domain I in complex with ADP | ||||||
![]() | Probable ATP-dependent RNA helicase DDX5 | ||||||
![]() | HYDROLASE / RNA HELICASE / DEAD / ADP / ATP-binding / Nucleotide-binding / RNA-binding / Helicase / Methylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / Spliceosome / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() MH2 domain binding / miRNA transcription / regulation of skeletal muscle cell differentiation / positive regulation of DNA damage response, signal transduction by p53 class mediator / primary miRNA binding / alternative mRNA splicing, via spliceosome / primary miRNA processing / regulation of viral genome replication / pre-mRNA binding / regulation of androgen receptor signaling pathway ...MH2 domain binding / miRNA transcription / regulation of skeletal muscle cell differentiation / positive regulation of DNA damage response, signal transduction by p53 class mediator / primary miRNA binding / alternative mRNA splicing, via spliceosome / primary miRNA processing / regulation of viral genome replication / pre-mRNA binding / regulation of androgen receptor signaling pathway / Replication of the SARS-CoV-1 genome / myoblast differentiation / mRNA transcription / nuclear-transcribed mRNA catabolic process / regulation of osteoblast differentiation / nuclear androgen receptor binding / SMAD binding / regulation of alternative mRNA splicing, via spliceosome / androgen receptor signaling pathway / R-SMAD binding / intrinsic apoptotic signaling pathway by p53 class mediator / epithelial to mesenchymal transition / estrogen receptor signaling pathway / BMP signaling pathway / ribonucleoprotein complex binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / SUMOylation of transcription cofactors / mRNA 3'-UTR binding / promoter-specific chromatin binding / mRNA splicing, via spliceosome / calcium-dependent protein binding / rhythmic process / Replication of the SARS-CoV-2 genome / Estrogen-dependent gene expression / RNA helicase activity / calmodulin binding / RNA helicase / nuclear speck / ribonucleoprotein complex / nucleolus / regulation of transcription by RNA polymerase II / enzyme binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Karlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wikstrom, M. / Wisniewska, M. / Schuler, H. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Comparative Structural Analysis of Human DEAD-Box RNA Helicases Authors: Schutz, P. / Karlberg, T. / van den Berg, S. / Collins, R. / Lehtio, L. / Hogbom, M. / Holmberg-Schiavone, L. / Tempel, W. / Park, H.W. / Hammarstrom, M. / Moche, M. / Thorsell, A.G. / Schuler, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.1 KB | Display | ![]() |
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PDB format | ![]() | 82.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 26.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2g9nC ![]() 2p6nC ![]() 2pl3C ![]() 2rb4C ![]() 3b7gC ![]() 3berC ![]() 3borC ![]() 3dkpC ![]() 3iuyC ![]() 3ly5C ![]() 2i4iS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 71 - 304 / Label seq-ID: 6 - 239
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Components
#1: Protein | Mass: 27271.418 Da / Num. of mol.: 2 / Fragment: DOMAIN I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17844, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 17.5% PEG3350, 0.25M Lithium Sulfate, 0.1M Bis-Tris, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 30, 2008 / Details: mirrors |
Radiation | Monochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→35 Å / Num. all: 16601 / Num. obs: 16601 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.142 / Rsym value: 0.188 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 4 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 2.44 / Num. unique all: 1211 / Rsym value: 0.728 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2I4I Resolution: 2.6→31.91 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.866 / SU B: 12.161 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.667 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.991 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→31.91 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3157 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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