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- PDB-4m1c: Crystal Structure Analysis of Fab-Bound Human Insulin Degrading E... -
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Basic information
Entry | Database: PDB / ID: 4m1c | ||||||
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Title | Crystal Structure Analysis of Fab-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Amyloid-Beta (1-40) | ||||||
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![]() | HYDROLASE / Zinc metalloprotease | ||||||
Function / homology | ![]() insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury ...insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / ubiquitin-modified protein reader activity / ciliary rootlet / Lysosome Vesicle Biogenesis / insulin binding / PTB domain binding / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / regulation of aerobic respiration / : / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / peptide catabolic process / suckling behavior / nuclear envelope lumen / dendrite development / amyloid-beta clearance / COPII-coated ER to Golgi transport vesicle / presynaptic active zone / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / peroxisomal matrix / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / amyloid-beta metabolic process / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / forebrain development / Notch signaling pathway / Insulin receptor recycling / Mitochondrial protein degradation / neuron projection maintenance / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / cholesterol metabolic process / positive regulation of mitotic cell cycle / response to interleukin-1 / adult locomotory behavior / extracellular matrix organization / axonogenesis / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / proteolysis involved in protein catabolic process / dendritic shaft / learning / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / endosome lumen / astrocyte activation / Peroxisomal protein import / positive regulation of JNK cascade / Post-translational protein phosphorylation / peptide binding / synapse organization / regulation of long-term neuronal synaptic plasticity / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McCord, L.M. / Liang, W. / Farcasanu, M. / Scherpelz, K. / Meredith, S.C. / Koide, S. / Tang, W.J. | ||||||
![]() | ![]() Title: Crystal Structure Analysis of Fab-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Amyloid-Beta (1-40) Authors: McCord, L.A. / Liang, W. / Farcasanu, M. / Scherpelz, K. / Meredith, S.C. / Koide, S. / Tang, W.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 889.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 494 KB | Display | ![]() |
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Full document | ![]() | 520.2 KB | Display | |
Data in XML | ![]() | 87.8 KB | Display | |
Data in CIF | ![]() | 117.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4iofS S: Starting model for refinement |
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Similar structure data |
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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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 114560.578 Da / Num. of mol.: 2 / Mutation: E111Q Source method: isolated from a genetically manipulated source Details: Cysteine-Free / Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 28201.670 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Specific antigen-binding fragment (Fab, light chain) synthetically engineered to target Human Insulin Degrading Enzyme Source: (synth.) ![]() #3: Antibody | Mass: 25982.098 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Specific antigen-binding fragment (Fab, heavy chain) synthetically engineered to target Human Insulin Degrading Enzyme Source: (synth.) ![]() #4: Protein/peptide | Mass: 4335.852 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Amyloid-Beta (1-40) / Source: (synth.) ![]() #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.65 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Sodium cacodylate, pH6.5, 0.2M MgCl2, 10% PEG-3000, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2013 |
Radiation | Monochromator: MAR CCD / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→49.1 Å / Num. all: 35563 / Num. obs: 35563 / % possible obs: 96.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 52.45 Å2 / Rmerge(I) obs: 0.159 |
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.68 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4IOF Resolution: 3.5007→49.064 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 26.98 / 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: 3.5007→49.064 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.9556 Å / Origin y: -8.5682 Å / Origin z: -98.8944 Å
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Refinement TLS group | Selection details: all |