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Yorodumi- PDB-3l33: Human mesotrypsin complexed with amyloid precursor protein inhibi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l33 | ||||||
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Title | Human mesotrypsin complexed with amyloid precursor protein inhibitor(APPI) | ||||||
Components |
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Keywords | Hydrolase/Cell Adhesion / Human mesotrypsin / alzheimer's amyloid precursor protein inhibitor / APPI / Serine protease inhibitor / Hydrolase-Cell Adhesion complex | ||||||
Function / homology | Function and homology information Uptake of dietary cobalamins into enterocytes / regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / antimicrobial humoral response / microglia development / Alpha-defensins / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands ...Uptake of dietary cobalamins into enterocytes / regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / antimicrobial humoral response / microglia development / Alpha-defensins / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of Wnt signaling pathway / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / zymogen activation / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Antimicrobial peptides / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein serine/threonine kinase binding / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / : / nuclear envelope lumen / suckling behavior / modulation of excitatory postsynaptic potential / presynaptic active zone / dendrite development / COPII-coated ER to Golgi transport vesicle / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Mitochondrial protein degradation / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / intracellular copper ion homeostasis / regulation of multicellular organism growth / negative regulation of long-term synaptic potentiation / negative regulation of neuron differentiation / ECM proteoglycans / smooth endoplasmic reticulum / endothelial cell migration / trypsin / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / Notch signaling pathway / digestion / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / neuron projection maintenance / serine-type peptidase activity / cholesterol metabolic process / response to interleukin-1 / positive regulation of glycolytic process / positive regulation of mitotic cell cycle / extracellular matrix organization / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / platelet alpha granule lumen / locomotory behavior / positive regulation of peptidyl-threonine phosphorylation / learning / positive regulation of interleukin-1 beta production / central nervous system development / positive regulation of long-term synaptic potentiation / endosome lumen / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / synapse organization / regulation of long-term neuronal synaptic plasticity / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / serine-type endopeptidase inhibitor activity / neuromuscular junction / recycling endosome / cognition / positive regulation of inflammatory response / Golgi lumen / neuron cellular homeostasis / endocytosis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.48 Å | ||||||
Authors | Salameh, M.A. / Soares, A.S. / Radisky, E.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Determinants of affinity and proteolytic stability in interactions of Kunitz family protease inhibitors with mesotrypsin. Authors: Salameh, M.A. / Soares, A.S. / Navaneetham, D. / Sinha, D. / Walsh, P.N. / Radisky, E.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l33.cif.gz | 430.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l33.ent.gz | 366.9 KB | Display | PDB format |
PDBx/mmJSON format | 3l33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/3l33 ftp://data.pdbj.org/pub/pdb/validation_reports/l3/3l33 | 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 24257.457 Da / Num. of mol.: 4 / Fragment: Trypsin-3 / Mutation: S195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: BL21(DE3) / Gene: PRSS3, PRSS4, TRY3, TRY4 / Production host: Escherichia coli (E. coli) / References: UniProt: P35030, trypsin #2: Protein | Mass: 5819.501 Da / Num. of mol.: 4 / Fragment: UNP residues 290-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Pichia pastoris (fungus) / References: UniProt: P05067 #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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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: 3.32 Å3/Da / Density % sol: 62.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 4M sodium formate solution, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.48→23.702 Å / Num. all: 57050 / Num. obs: 57050 / % possible obs: 99.3 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.263 / Rsym value: 0.263 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.48→2.61 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.024 / Mean I/σ(I) obs: 0.3 / Num. measured all: 98361 / Num. unique all: 7901 / Rsym value: 0.02353 / % possible all: 95.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→23.702 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.843 / Stereochemistry target values: mlhl
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Solvent computation | Bsol: 73.674 Å2 / ksol: 0.426 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 222.85 Å2 / Biso mean: 44.887 Å2 / Biso min: 10.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.48→23.702 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.48→2.488 Å / Total num. of bins used: 110
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