+Open data
-Basic information
Entry | Database: PDB / ID: 8ae4 | |||||||||
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Title | Crystal structure of human legumain in complex with Clitocypin 2 | |||||||||
Components |
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Keywords | HYDROLASE / cysteine protease / ligase / asparaginyl endopeptidase / AEP / inhibitor / exosite / active site / substrate | |||||||||
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 / endolysosome lumen / response to acidic pH ...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 / endolysosome lumen / response to acidic pH / activation of cysteine-type endopeptidase activity / 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 / 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) Clitocybe nebularis (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | |||||||||
Authors | Elamin, T. / Brandstetter, H. / Dall, E. | |||||||||
Funding support | Austria, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Structural and functional studies of legumain-mycocypin complexes revealed a competitive, exosite-regulated mode of interaction. Authors: Elamin, T. / Santos, N.P. / Briza, P. / Brandstetter, H. / Dall, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ae4.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ae4.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ae4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ae4_validation.pdf.gz | 855.3 KB | Display | wwPDB validaton report |
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Full document | 8ae4_full_validation.pdf.gz | 861.2 KB | Display | |
Data in XML | 8ae4_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 8ae4_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/8ae4 ftp://data.pdbj.org/pub/pdb/validation_reports/ae/8ae4 | HTTPS FTP |
-Related structure data
Related structure data | 8ae5C 7o50S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30147.865 Da / Num. of mol.: 1 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: 18039.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clitocybe nebularis (fungus) / Gene: clt2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3Y9I4 | ||||
#3: 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 | ||||
#4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate pH 4.5, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→41.82 Å / Num. obs: 40893 / % possible obs: 97 % / Redundancy: 7.74 % / Biso Wilson estimate: 22.87 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.14 / Net I/σ(I): 11.21 |
Reflection shell | Resolution: 1.79→1.9 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 5729 / CC1/2: 0.49 / Rrim(I) all: 1.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7o50 Resolution: 1.79→41.53 Å / SU ML: 0.2326 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.8157 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→41.53 Å
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Refine LS restraints |
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LS refinement shell |
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