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Yorodumi- PDB-4ral: Crystal structure of insulin degrading enzyme in complex with mac... -
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-Basic information
Entry | Database: PDB / ID: 4ral | |||||||||
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Title | Crystal structure of insulin degrading enzyme in complex with macrophage inflammatory protein 1 beta | |||||||||
Components |
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Keywords | HYDROLASE/CYTOKINE / IDE / MIP1alpha / metal-binding / metalloprotease / chemotaxis / inflammatory response / HYDROLASE-CYTOKINE complex | |||||||||
Function / homology | Function and homology information CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / CCR5 chemokine receptor binding / negative regulation by host of viral transcription / CCR chemokine receptor binding / amyloid-beta clearance by cellular catabolic process ...CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / CCR5 chemokine receptor binding / negative regulation by host of viral transcription / CCR chemokine receptor binding / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / positive regulation of calcium ion transport / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / insulin binding / regulation of aerobic respiration / establishment or maintenance of cell polarity / peptide catabolic process / amyloid-beta clearance / Interleukin-10 signaling / peroxisomal matrix / amyloid-beta metabolic process / Insulin receptor recycling / positive regulation of calcium-mediated signaling / peptide binding / proteolysis involved in protein catabolic process / cytokine activity / Peroxisomal protein import / response to virus / protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / response to toxic substance / metalloendopeptidase activity / positive regulation of protein catabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / virus receptor activity / positive regulation of protein binding / insulin receptor signaling pathway / cell-cell signaling / peroxisome / basolateral plasma membrane / endopeptidase activity / G alpha (i) signalling events / cell adhesion / positive regulation of cell migration / Ub-specific processing proteases / inflammatory response / immune response / external side of plasma membrane / cell surface / signal transduction / protein homodimerization activity / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.148 Å | |||||||||
Authors | Liang, W.G. / Ren, M. / Guo, Q. / Tang, W.J. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Structures of human CCL18, CCL3, and CCL4 reveal molecular determinants for quaternary structures and sensitivity to insulin-degrading enzyme. Authors: Liang, W.G. / Ren, M. / Zhao, F. / 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 | 4ral.cif.gz | 788.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ral.ent.gz | 647 KB | Display | PDB format |
PDBx/mmJSON format | 4ral.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ral_validation.pdf.gz | 459.3 KB | Display | wwPDB validaton report |
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Full document | 4ral_full_validation.pdf.gz | 481.9 KB | Display | |
Data in XML | 4ral_validation.xml.gz | 65.4 KB | Display | |
Data in CIF | 4ral_validation.cif.gz | 88 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/4ral ftp://data.pdbj.org/pub/pdb/validation_reports/ra/4ral | HTTPS FTP |
-Related structure data
Related structure data | 3tn2C 4mheC 4ra8C 3cwwS 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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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, C178A, 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: IDE / Production host: Escherichia coli (E. coli) / References: UniProt: P14735, insulysin #2: Protein | Mass: 7824.742 Da / Num. of mol.: 2 / Fragment: UNP residues 24-92 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCL4, LAG1, MIP1B, SCYA4 / Production host: Escherichia coli (E. coli) / References: UniProt: P13236 #3: Chemical | #4: 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: 3.71 Å3/Da / Density % sol: 66.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 13% PEG5000 MME, 100 mM HEPES, pH 7.0, 10% Tacsimate, 10% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2010 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.148→48.263 Å / Num. all: 59484 / Num. obs: 59484 / % possible obs: 95.5 % / Observed criterion σ(F): 3.06 / Observed criterion σ(I): 3.06 / Redundancy: 4.3 % / Rmerge(I) obs: 0.209 / Rsym value: 0.216 / Net I/σ(I): 7.4 |
Reflection shell | Highest resolution: 3.148 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CWW Resolution: 3.148→48.263 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 25.9 / 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: 3.148→48.263 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: -104.0282 Å / Origin y: 23.6136 Å / Origin z: -5.9716 Å
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Refinement TLS group | Selection details: all |