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Yorodumi- PDB-3n56: Crystal Structure of human Insulin-degrading enzyme (IDE) in comp... -
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-Basic information
Entry | Database: PDB / ID: 3n56 | ||||||
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Title | Crystal Structure of human Insulin-degrading enzyme (IDE) in complex with human B-type natriuretic peptide (BNP) | ||||||
Components |
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Keywords | HYDROLASE/HORMONE / INSULYSIN / INSULINASE / A-BETA DEGRADING ENZYME / CRYPTIDASE / HYDROLASE / HORMONE / DISEASE MUTATION / DIABETES MELLITUS / INSULIN / CARDIAC / SECRETED / PROTEASE / DISULFIDE BOND / METALLOPROTEASE / HUMAN INSULIN-DEGRADNG ENZYME / METAL-BINDING / NATRIURETIC PEPTIDE / NATRIURETIC FACTOR / CARDIOVASCULAR REGULATION / HYDROLASE-HORMONE complex | ||||||
Function / homology | Function and homology information diuretic hormone activity / body fluid secretion / receptor guanylyl cyclase signaling pathway / positive regulation of renal sodium excretion / cGMP biosynthetic process / insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / regulation of vascular permeability ...diuretic hormone activity / body fluid secretion / receptor guanylyl cyclase signaling pathway / positive regulation of renal sodium excretion / cGMP biosynthetic process / insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / regulation of vascular permeability / cardiac conduction system development / amyloid-beta clearance by cellular catabolic process / positive regulation of urine volume / hormone catabolic process / bradykinin catabolic process / negative regulation of systemic arterial blood pressure / hormone receptor binding / ubiquitin-modified protein reader activity / insulin binding / regulation of aerobic respiration / peptide catabolic process / amyloid-beta clearance / cGMP-mediated signaling / peroxisomal matrix / neuropeptide signaling pathway / amyloid-beta metabolic process / Insulin receptor recycling / blood vessel diameter maintenance / negative regulation of angiogenesis / proteolysis involved in protein catabolic process / Peroxisomal protein import / peptide binding / protein catabolic process / negative regulation of cell growth / hormone activity / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / regulation of blood pressure / peroxisome / positive regulation of protein catabolic process / vasodilation / protein folding / positive regulation of protein binding / virus receptor activity / insulin receptor signaling pathway / basolateral plasma membrane / endopeptidase activity / cell surface receptor signaling pathway / Ub-specific processing proteases / external side of plasma membrane / signaling receptor binding / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.102 Å | ||||||
Authors | Funke, T. / Guo, Q. / Tang, W.-J. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of human Insulin-degrading enzyme (IDE) in complex with human B-type natriuretic peptide (BNP) Authors: Ralat, L.A. / Funke, T. / Ren, M. / Guo, Q. / Dickey, D.M. / Potter, L.R. / Tang, W.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n56.cif.gz | 396.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n56.ent.gz | 313.6 KB | Display | PDB format |
PDBx/mmJSON format | 3n56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/3n56 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/3n56 | HTTPS FTP |
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-Related structure data
Related structure data | 3cwwS S: Starting model for refinement |
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Similar 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: 114560.578 Da / Num. of mol.: 2 / Fragment: UNP residues 42-1019 Mutation: C110L, E111Q, C171S, C178S, C257V, C414L, C573N, C590S, C789S, C812A, C819A, C904S, C966N, C974A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HCG_1810909, IDE, RP11-366I13.1-001 / Plasmid: PPROEX-H6 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: P14735, insulysin #2: Protein/peptide | Mass: 3474.120 Da / Num. of mol.: 2 / Fragment: UNP residues 103-134 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NPPB / References: UniProt: P16860 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 13% PEGMME-5000, 10% TACSIMATE, 10% DIOXANE, 100 mM Na-HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2009 / Details: MIRRORS |
Radiation | Monochromator: Si(111) AND Si(220)-SAGITALLY FOCUSED DOUBLE CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 3.102→50 Å / Num. all: 63372 / Num. obs: 62152 / % possible obs: 96.54 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.20299 / Rsym value: 0.078 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 3.102→3.182 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4642 / Rsym value: 0.462 / % possible all: 98.64 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3cww Resolution: 3.102→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 16.517 / SU ML: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.385 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.43 Å2 / Biso mean: 54.03 Å2 / Biso min: 36.51 Å2
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Refinement step | Cycle: LAST / Resolution: 3.102→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.102→3.182 Å / Total num. of bins used: 20
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