+Open data
-Basic information
Entry | Database: PDB / ID: 5c97 | |||||||||
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Title | Insulin regulated aminopeptidase | |||||||||
Components | Leucyl-cystinyl aminopeptidaseLeucyl/cystinyl aminopeptidase | |||||||||
Keywords | HYDROLASE / aminopeptidase / antigen presentation / IRAP | |||||||||
Function / homology | Function and homology information cystinyl aminopeptidase / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / negative regulation of cold-induced thermogenesis / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / early endosome lumen / female pregnancy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Endosomal/Vacuolar pathway ...cystinyl aminopeptidase / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / negative regulation of cold-induced thermogenesis / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / early endosome lumen / female pregnancy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Endosomal/Vacuolar pathway / peptide binding / protein catabolic process / cytoplasmic vesicle membrane / regulation of blood pressure / protein polyubiquitination / metallopeptidase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell-cell signaling / lysosomal membrane / perinuclear region of cytoplasm / signal transduction / proteolysis / zinc ion binding / extracellular region / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.37 Å | |||||||||
Authors | Mpakali, A. / Saridakis, E. / Harlos, K. / Zhao, Y. / Stratikos, E. | |||||||||
Citation | Journal: J Immunol. / Year: 2015 Title: Crystal Structure of Insulin-Regulated Aminopeptidase with Bound Substrate Analogue Provides Insight on Antigenic Epitope Precursor Recognition and Processing. Authors: Mpakali, A. / Saridakis, E. / Harlos, K. / Zhao, Y. / Papakyriakou, A. / Kokkala, P. / Georgiadis, D. / Stratikos, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c97.cif.gz | 367.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c97.ent.gz | 290.8 KB | Display | PDB format |
PDBx/mmJSON format | 5c97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/5c97 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/5c97 | HTTPS FTP |
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-Related structure data
Related structure data | 4z7iC 4p8qS C: citing same article (ref.) 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: 104217.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LNPEP, OTASE / Production host: Homo sapiens (human) / References: UniProt: Q9UIQ6, cystinyl aminopeptidase #2: 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 #3: Chemical | #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.1M bicine/Trizma base, 0.2 M sodium L-glutamate, 0.2M DL-alanine, 0.2M glycine, 0.2M DL-lysine HCl, 0.2M DL-serine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 3.37→68.27 Å / Num. obs: 33870 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 3.37→3.46 Å / Redundancy: 7 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P8Q Resolution: 3.37→68.204 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.54 / 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: 3.37→68.204 Å
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Refine LS restraints |
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LS refinement shell |
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