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- PDB-5ctr: Crystal structure of human SART3 HAT-C domain-human USP4 DUSP-UBL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ctr | ||||||
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Title | Crystal structure of human SART3 HAT-C domain-human USP4 DUSP-UBL domain complex | ||||||
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![]() | IMMUNE SYSTEM / NUCLEAR PROTEIN / RNA BINDING PROTEIN / HYDROLASE / Nuclear complex / Deubiquitinase | ||||||
Function / homology | ![]() adenosine receptor binding / U6atac snRNA binding / ASAP complex / U4 snRNA binding / protein localization to cell surface / TNFR1-induced proapoptotic signaling / hematopoietic stem cell proliferation / transcription elongation-coupled chromatin remodeling / ubiquitin-specific protease binding / protein deubiquitination ...adenosine receptor binding / U6atac snRNA binding / ASAP complex / U4 snRNA binding / protein localization to cell surface / TNFR1-induced proapoptotic signaling / hematopoietic stem cell proliferation / transcription elongation-coupled chromatin remodeling / ubiquitin-specific protease binding / protein deubiquitination / homeostasis of number of cells / spliceosomal tri-snRNP complex assembly / U6 snRNA binding / spliceosomal snRNP assembly / Cajal body / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / regulation of protein stability / cell morphogenesis / mRNA splicing, via spliceosome / nucleosome assembly / histone binding / regulation of gene expression / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / Ub-specific processing proteases / nuclear speck / proteolysis / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, J.K. / Kim, E.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for recruiting and shuttling of the spliceosomal deubiquitinase USP4 by SART3 Authors: Park, J.K. / Das, T. / Song, E.J. / Kim, E.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.1 KB | Display | ![]() |
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PDB format | ![]() | 179 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 466.7 KB | Display | ![]() |
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Full document | ![]() | 511.3 KB | Display | |
Data in XML | ![]() | 42.1 KB | Display | |
Data in CIF | ![]() | 57 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ctqSC ![]() 5cttC 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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Components
#1: Protein | Mass: 39913.336 Da / Num. of mol.: 2 / Fragment: UNP residues 278-611 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 27017.449 Da / Num. of mol.: 2 / Fragment: UNP residues 1-230 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 67.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM MES pH 6.8, 200 mM magnesium chloride, 15% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 41894 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.26 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CTQ Resolution: 3.012→50 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 33.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.62 Å2 / ksol: 0.247 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.012→50 Å
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Refine LS restraints |
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LS refinement shell |
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