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Yorodumi- PDB-3u8b: Functionally selective inhibition of Group IIA phospholipase A2 r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u8b | ||||||
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Title | Functionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism | ||||||
Components | Phospholipase A2, membrane associated | ||||||
Keywords | HYDROLASE / secreted phospholipase A2 / Phospholipase A2 activity | ||||||
Function / homology | Function and homology information regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / intestinal stem cell homeostasis / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA ...regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / intestinal stem cell homeostasis / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / positive regulation of macrophage derived foam cell differentiation / phosphatidylcholine metabolic process / phospholipase A2 activity / calcium-dependent phospholipase A2 activity / low-density lipoprotein particle remodeling / phospholipase A2 / Antimicrobial peptides / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / secretory granule / phospholipid binding / positive regulation of inflammatory response / killing of cells of another organism / mitochondrial outer membrane / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å | ||||||
Authors | Lee, L.K. / Bryant, K.J. / Bouveret, R. / Lei, P.-W. / Duff, A.P. / Harrop, S.J. / Huang, E.P. / Harvey, R.P. / Gelb, M.H. / Gray, P.P. ...Lee, L.K. / Bryant, K.J. / Bouveret, R. / Lei, P.-W. / Duff, A.P. / Harrop, S.J. / Huang, E.P. / Harvey, R.P. / Gelb, M.H. / Gray, P.P. / Curmi, P.M. / Cunningham, A.M. / Church, W.B. / Scott, K.F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Selective Inhibition of Human Group IIA-secreted Phospholipase A2 (hGIIA) Signaling Reveals Arachidonic Acid Metabolism Is Associated with Colocalization of hGIIA to Vimentin in Rheumatoid Synoviocytes. Authors: Lee, L.K. / Bryant, K.J. / Bouveret, R. / Lei, P.W. / Duff, A.P. / Harrop, S.J. / Huang, E.P. / Harvey, R.P. / Gelb, M.H. / Gray, P.P. / Curmi, P.M. / Cunningham, A.M. / Church, W.B. / Scott, K.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u8b.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u8b.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 3u8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/3u8b ftp://data.pdbj.org/pub/pdb/validation_reports/u8/3u8b | HTTPS FTP |
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-Related structure data
-Links
-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: 13945.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G2A, PLA2B, PLA2L, RASF-A / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P14555, phospholipase A2 | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1 M Tris HCl pH 7.4, 10 mM CaCl2, 0.5 mM Beta-octyl glucoside and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2006 |
Radiation | Monochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 2.299→24.446 Å / Num. all: 6955 / Num. obs: 6906 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.299→24.446 Å / SU ML: 0.6 / σ(F): 1.36 / Phase error: 27.02 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.024 Å2 / ksol: 0.433 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.299→24.446 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.299→2.8958 Å
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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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