[English] 日本語
Yorodumi- PDB-5ctr: Crystal structure of human SART3 HAT-C domain-human USP4 DUSP-UBL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ctr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human SART3 HAT-C domain-human USP4 DUSP-UBL domain complex | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / NUCLEAR PROTEIN / RNA BINDING PROTEIN / HYDROLASE / Nuclear complex / Deubiquitinase | ||||||
Function / homology | Function and homology information 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 / Cajal body / U6 snRNA binding / spliceosomal snRNP assembly / 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 / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.012 Å | ||||||
Authors | Park, J.K. / Kim, E.E. | ||||||
Funding support | Korea, Republic Of, 1items
| ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2016 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ctr.cif.gz | 224.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ctr.ent.gz | 179 KB | Display | PDB format |
PDBx/mmJSON format | 5ctr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/5ctr ftp://data.pdbj.org/pub/pdb/validation_reports/ct/5ctr | HTTPS FTP |
---|
-Related structure data
Related structure data | 5ctqSC 5cttC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Gene: SART3, KIAA0156, TIP110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15020 #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.) Homo sapiens (human) / Gene: USP4, UNP, UNPH / Production host: Escherichia coli (E. coli) / References: UniProt: Q13107, ubiquitinyl hydrolase 1 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 67.58 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.012→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|