[English] 日本語
Yorodumi- PDB-3vfq: Human PARP14 (ARTD8, BAL2) - macro domains 1 and 2 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vfq | ||||||
---|---|---|---|---|---|---|---|
Title | Human PARP14 (ARTD8, BAL2) - macro domains 1 and 2 in complex with adenosine-5-diphosphoribose | ||||||
Components | Poly [ADP-ribose] polymerase 14 | ||||||
Keywords | TRANSFERASE / ADP-RIBOSE / PARP14 / MACRO / BAL2 / ARTD8 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases ...positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Karlberg, T. / Thorsell, A.G. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Weigelt, J. / Schuler, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Structure / Year: 2013 Title: Recognition of Mono-ADP-Ribosylated ARTD10 Substrates by ARTD8 Macrodomains. Authors: Forst, A.H. / Karlberg, T. / Herzog, N. / Thorsell, A.G. / Gross, A. / Feijs, K.L. / Verheugd, P. / Kursula, P. / Nijmeijer, B. / Kremmer, E. / Kleine, H. / Ladurner, A.G. / Schuler, H. / Luscher, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3vfq.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3vfq.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 3vfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/3vfq ftp://data.pdbj.org/pub/pdb/validation_reports/vf/3vfq | HTTPS FTP |
---|
-Related structure data
Related structure data | 3q6zSC 3q71SC 3v2bC 4abkC 4ablC 4d86C C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 44707.414 Da / Num. of mol.: 1 / Fragment: Macro domains 1 and 2 (UNP residues 784-1196) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAL2, KIAA1268, PARP14 / Plasmid: PNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PRARE / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase |
---|---|
#2: Chemical | ChemComp-AR6 / [( |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.47 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20% PEG3350, 0.2M SODIUM-THIOCYANATE, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93928 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2010 |
Radiation | Monochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93928 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 10514 / Num. obs: 10514 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.175 / Rsym value: 0.132 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 2.3 / Num. unique all: 750 / Rsym value: 0.652 / % possible all: 99.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3Q6Z AND 3Q71 Resolution: 2.8→46.62 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.866 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→46.62 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
|