[English] 日本語
Yorodumi- PDB-8q1k: Structural analysis of PLD3 reveals insights into the mechanism o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q1k | ||||||
---|---|---|---|---|---|---|---|
Title | Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation | ||||||
Components | 5'-3' exonuclease PLD3 | ||||||
Keywords | DNA BINDING PROTEIN / PLD3 / structural biology / lysosome / DNA/RNA degradation / phospholipase D / 5' exonuclease | ||||||
Function / homology | Function and homology information spleen exonuclease / Synthesis of PG / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / phospholipase D activity / immune system process / regulation of cytokine production involved in inflammatory response / Role of phospholipids in phagocytosis / lysosomal lumen / late endosome membrane ...spleen exonuclease / Synthesis of PG / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / phospholipase D activity / immune system process / regulation of cytokine production involved in inflammatory response / Role of phospholipids in phagocytosis / lysosomal lumen / late endosome membrane / early endosome membrane / inflammatory response / lysosomal membrane / Golgi membrane / endoplasmic reticulum membrane / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.51 Å | ||||||
Authors | Roske, Y. / Daumke, O. / Damme, M. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2024 Title: Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation. Authors: Roske, Y. / Cappel, C. / Cremer, N. / Hoffmann, P. / Koudelka, T. / Tholey, A. / Heinemann, U. / Daumke, O. / Damme, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8q1k.cif.gz | 418.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8q1k.ent.gz | 339.5 KB | Display | PDB format |
PDBx/mmJSON format | 8q1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q1k_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8q1k_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 8q1k_validation.xml.gz | 46.5 KB | Display | |
Data in CIF | 8q1k_validation.cif.gz | 71.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/8q1k ftp://data.pdbj.org/pub/pdb/validation_reports/q1/8q1k | HTTPS FTP |
-Related structure data
Related structure data | 8q1xC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46945.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IV08 |
---|
-Sugars , 3 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source | ||
---|---|---|---|
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
-Non-polymers , 4 types, 1243 molecules
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PO4 / #7: Chemical | ChemComp-MN / #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 17% PEG 4000, 0.02 M NaI, 0.6 M Ammonium sulfate |
---|
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→44.65 Å / Num. obs: 200406 / % possible obs: 97.8 % / Redundancy: 3.77 % / CC1/2: 0.99 / Rrim(I) all: 0.0074 / Net I/σ(I): 10.71 |
Reflection shell | Resolution: 1.51→1.61 Å / Num. unique obs: 31270 / CC1/2: 0.26 / Rrim(I) all: 0.228 / % possible all: 94.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.51→44.65 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.719 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.012 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.94 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.51→44.65 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|