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- PDB-8g25: Crystal Structure of Cathepsin-G and Neutrophil Elastase Inhibite... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8g25 | ||||||
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Title | Crystal Structure of Cathepsin-G and Neutrophil Elastase Inhibited by S. aureus EapH2 at pH 7.5 | ||||||
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![]() | HYDROLASE/INHIBITOR / Protease Inhibitor / Immune Evasion / Neutrophil / S. aureus / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / purinergic nucleotide receptor signaling pathway / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / negative regulation of T cell activation ...cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / purinergic nucleotide receptor signaling pathway / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / negative regulation of T cell activation / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / caspase binding / negative regulation of chemokine production / Suppression of apoptosis / protein metabolic process / neutrophil activation / positive regulation of platelet aggregation / Interleukin-1 processing / Antimicrobial peptides / cytokine binding / pyroptotic inflammatory response / Activation of Matrix Metalloproteinases / neutrophil-mediated killing of gram-negative bacterium / monocyte chemotaxis / Collagen degradation / extracellular matrix disassembly / angiotensin maturation / defense response to fungus / Metabolism of Angiotensinogen to Angiotensins / Pyroptosis / Purinergic signaling in leishmaniasis infection / phagocytosis / response to UV / transcription repressor complex / phagocytic vesicle / Degradation of the extracellular matrix / serine-type peptidase activity / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / protein catabolic process / protein processing / platelet activation / cytokine-mediated signaling pathway / negative regulation of inflammatory response / cytoplasmic stress granule / intracellular calcium ion homeostasis / specific granule lumen / transcription corepressor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of immune response / azurophil granule lumen / heparin binding / peptidase activity / antibacterial humoral response / cellular response to lipopolysaccharide / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / endopeptidase activity / protease binding / response to lipopolysaccharide / receptor ligand activity / lysosome / defense response to Gram-positive bacterium / defense response to bacterium / immune response / protein phosphorylation / intracellular membrane-bounded organelle / serine-type endopeptidase activity / Neutrophil degranulation / cell surface / negative regulation of transcription by RNA polymerase II / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mishra, N.B. / Geisbrecht, B.V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Simultaneous inhibition of two neutrophil serine proteases by the S. aureus innate immune evasion protein EapH2. Authors: Mishra, N. / Herdendorf, T.J. / Prakash, O. / Geisbrecht, B.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 657 KB | Display | ![]() |
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PDB format | ![]() | 541.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 498 KB | Display | ![]() |
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Full document | ![]() | 527.5 KB | Display | |
Data in XML | ![]() | 63.5 KB | Display | |
Data in CIF | ![]() | 89.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8g24C ![]() 8g26C ![]() 8gdgC ![]() 8gdhC ![]() 1au8S ![]() 1hneS ![]() 1yn5S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25397.131 Da / Num. of mol.: 3 / Fragment: C-terminal truncation (UNP residues 21-243) / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 23318.982 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 13123.912 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SAV0981 / Production host: ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, 0.2 M lithium sulfate, 26% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 149744 / % possible obs: 98.1 % / Redundancy: 3.3 % / CC1/2: 0.979 / Rpim(I) all: 0.075 / Χ2: 0.111 / Net I/σ(I): 5.1 / Num. measured all: 951665 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 1AU8, 1HNE, & 1YN5 Resolution: 1.8→46.13 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.17 / Phase error: 35.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→46.13 Å
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Refine LS restraints |
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LS refinement shell |
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