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Yorodumi- PDB-4n6o: Crystal structure of reduced legumain in complex with cystatin E/M -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n6o | ||||||||||||
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Title | Crystal structure of reduced legumain in complex with cystatin E/M | ||||||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / complex / cysteine protease / inhibitor / legumain / asparaginyl endopeptidase / reactive center loop / papain / cathepsin / cancer / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / cornified envelope / endolysosome lumen ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / cornified envelope / endolysosome lumen / activation of cysteine-type endopeptidase activity / response to acidic pH / dendritic spine organization / positive regulation of monocyte chemotaxis / Trafficking and processing of endosomal TLR / positive regulation of endothelial cell chemotaxis / negative regulation of multicellular organism growth / cysteine-type endopeptidase inhibitor activity / cellular response to hepatocyte growth factor stimulus / associative learning / protein maturation / endopeptidase activator activity / anatomical structure morphogenesis / epidermis development / cellular response to calcium ion / MHC class II antigen presentation / positive regulation of mitotic cell cycle / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of long-term synaptic potentiation / tau protein binding / memory / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / apical part of cell / peptidase activity / negative regulation of neuron apoptotic process / lysosome / cysteine-type endopeptidase activity / negative regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||||||||
Authors | Dall, E. / Brandstetter, H. | ||||||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Structure and mechanism of an aspartimide-dependent Peptide ligase in human legumain. Authors: Dall, E. / Fegg, J.C. / Briza, P. / Brandstetter, H. | ||||||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n6o.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n6o.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 4n6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/4n6o ftp://data.pdbj.org/pub/pdb/validation_reports/n6/4n6o | HTTPS FTP |
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-Related structure data
Related structure data | 4n6lSC 4n6mC 4n6nC 4aw9S 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 , 2 types, 2 molecules AB
#1: Protein | Mass: 31643.551 Da / Num. of mol.: 1 / Fragment: UNP residues 26-303 / Mutation: N263Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGMN, PRSC1 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: Q99538, legumain |
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#2: Protein | Mass: 14924.931 Da / Num. of mol.: 1 / Fragment: UNP residues 29-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CST6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15828 |
-Sugars , 2 types, 2 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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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#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 2 types, 284 molecules
#5: Chemical | ChemComp-IOD / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES 147 AND 148 STARTED OUT AS ASP AND HIS. THE SIDECHAIN OF ASP ATTACKS THE FOLLOWING AMIDE ...RESIDUES 147 AND 148 STARTED OUT AS ASP AND HIS. THE SIDECHAIN OF ASP ATTACKS THE FOLLOWING AMIDE OF HIS TO FORM A SUCCINIMID |
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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: 2.4 Å3/Da / Density % sol: 48.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25 % PEG 4000, 100 mM MES pH 6.5, 200 mM potassium iodide, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.39 Å / Num. obs: 40857 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AW9, 4N6L Resolution: 1.8→44.48 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.863 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.139 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 24.407 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→44.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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