+Open data
-Basic information
Entry | Database: PDB / ID: 6ael | |||||||||
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Title | Crystal structure of ENPP1 in complex with 3'3'-cGAMP | |||||||||
Components | Ectonucleotide pyrophosphatase/phosphodiesterase 1, isoform CRA_d | |||||||||
Keywords | IMMUNOSUPPRESSANT / Enzyme / Phoshodiesterase / cGAMP / cGAS-STING / cyclic GMP-AMP | |||||||||
Function / homology | Function and homology information articular cartilage development / microglial cell migration / Vitamin B2 (riboflavin) metabolism / response to platelet-derived growth factor / ligamentous ossification / response to vitamin B6 / cellular response to sodium phosphate / GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity ...articular cartilage development / microglial cell migration / Vitamin B2 (riboflavin) metabolism / response to platelet-derived growth factor / ligamentous ossification / response to vitamin B6 / cellular response to sodium phosphate / GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / organic phosphonate metabolic process / inorganic diphosphate transport / post-embryonic forelimb morphogenesis / UTP diphosphatase activity / tooth mineralization / hematopoietic stem cell migration to bone marrow / leukocyte activation involved in inflammatory response / bone trabecula formation / phosphodiesterase I / bone growth / biomineral tissue development / dinucleotide phosphatase activity / coenzyme A diphosphatase activity / basal dendrite / sensory perception of temperature stimulus / coenzyme A catabolic process / nucleoside triphosphate catabolic process / vascular associated smooth muscle cell migration / nucleotide diphosphatase / inhibition of non-skeletal tissue mineralization / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / response to Gram-positive bacterium / magnesium ion homeostasis / diphosphate metabolic process / pyrophosphatase activity / endochondral bone morphogenesis / vitamin D3 metabolic process / intracellular phosphate ion homeostasis / central nervous system myelination / cementum mineralization / negative regulation of protein autophosphorylation / nucleoside triphosphate diphosphatase activity / vascular associated smooth muscle cell proliferation / bone mineralization involved in bone maturation / mucus secretion / response to sodium phosphate / sequestering of triglyceride / ATP diphosphatase activity / negative regulation of glycogen biosynthetic process / negative regulation of bone mineralization / sensory perception of mechanical stimulus / phosphate ion homeostasis / melanocyte differentiation / plasma cell differentiation / B-1 B cell homeostasis / phosphodiesterase I activity / artery development / microglia differentiation / scavenger receptor activity / bone remodeling / collagen-activated signaling pathway / cellular homeostasis / apoptotic process involved in development / endochondral ossification / apical dendrite / phosphoric diester hydrolase activity / negative regulation of glucose import / regulation of bone mineralization / hormone metabolic process / negative regulation of ossification / inflammatory response to antigenic stimulus / middle ear morphogenesis / adult walking behavior / phosphate-containing compound metabolic process / cartilage development / oligodendrocyte apoptotic process / : / aorta development / odontogenesis / exonuclease activity / axon regeneration / fat pad development / skin development / negative regulation of fat cell differentiation / smoothened signaling pathway / muscle cell cellular homeostasis / polysaccharide binding / hydrolase activity, acting on ester bonds / response to ATP / spinal cord development / fat cell differentiation / glucose import / bone mineralization / defense response to protozoan / phosphatase activity / response to magnesium ion / response to dietary excess / macrophage differentiation / T cell differentiation / 3',5'-cyclic-AMP phosphodiesterase activity Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Kato, K. / Nishimasu, H. / Hirano, S. / Hirano, H. / Ishitani, R. / Nureki, O. | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1. Authors: Kato, K. / Nishimasu, H. / Oikawa, D. / Hirano, S. / Hirano, H. / Kasuya, G. / Ishitani, R. / Tokunaga, F. / Nureki, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ael.cif.gz | 324.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ael.ent.gz | 257 KB | Display | PDB format |
PDBx/mmJSON format | 6ael.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/6ael ftp://data.pdbj.org/pub/pdb/validation_reports/ae/6ael | HTTPS FTP |
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-Related structure data
Related structure data | 6aekC 4gtwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 84816.156 Da / Num. of mol.: 1 / Mutation: T238A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Enpp1, mCG_9001 / Production host: Homo sapiens (human) / References: UniProt: G3X9S2, UniProt: P06802*PLUS |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar |
-Non-polymers , 6 types, 374 molecules
#4: Chemical | ChemComp-4BW / | ||||||||
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#5: Chemical | #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-EDO / #9: Water | ChemComp-HOH / | |
-Details
Sequence details | Protease recognition site |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 16% PEG3350, 0.1 M Bis-Tris propane, pH 8.5, 0.2 M NaBr and 0.1 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47 Å / Num. obs: 57243 / % possible obs: 100 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.751 / Num. unique obs: 57214 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GTW Resolution: 1.9→47 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→47 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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