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Yorodumi- PDB-4jbs: Crystal structure of the human Endoplasmic Reticulum Aminopeptida... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jbs | |||||||||
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Title | Crystal structure of the human Endoplasmic Reticulum Aminopeptidase 2 in complex with PHOSPHINIC PSEUDOTRIPEPTIDE inhibitor. | |||||||||
Components | Endoplasmic reticulum aminopeptidase 2 | |||||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Thermolysin-like catalytic domain / Hydrolase / Aminopeptidase / Zinc binding / Endoplasmic Reticulum / Hydrolase-Hydrolase Inhibitor complex | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / metallopeptidase activity ...Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / metallopeptidase activity / endopeptidase activity / adaptive immune response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / proteolysis / extracellular space / zinc ion binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.789 Å | |||||||||
Authors | Saridakis, E. / Birtley, J. / Stratikos, E. / Mavridis, I.M. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Rationally designed inhibitor targeting antigen-trimming aminopeptidases enhances antigen presentation and cytotoxic T-cell responses. Authors: Zervoudi, E. / Saridakis, E. / Birtley, J.R. / Seregin, S.S. / Reeves, E. / Kokkala, P. / Aldhamen, Y.A. / Amalfitano, A. / Mavridis, I.M. / James, E. / 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 | 4jbs.cif.gz | 373.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jbs.ent.gz | 297.6 KB | Display | PDB format |
PDBx/mmJSON format | 4jbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jbs_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 4jbs_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 4jbs_validation.xml.gz | 72.8 KB | Display | |
Data in CIF | 4jbs_validation.cif.gz | 97.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/4jbs ftp://data.pdbj.org/pub/pdb/validation_reports/jb/4jbs | HTTPS FTP |
-Related structure data
Related structure data | 4e36S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 111530.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP2, LRAP / Plasmid: pFASTBac-1 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q6P179, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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-Sugars , 3 types, 9 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-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 | ChemComp-NAG / |
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-Non-polymers , 4 types, 299 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: 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: 2.92 Å3/Da / Density % sol: 57.91 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% PEG 8000, 20% ethylene glycol, 69 mM MES, 31 mM imidazole.Drops incubated at 277 K before being transferred to 289 K, pH 6.5, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 25, 2012 |
Radiation | Monochromator: BARTELS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.789→49 Å / Num. all: 125739 / Num. obs: 119216 / % possible obs: 94.81 % / Observed criterion σ(I): -5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.065 |
Reflection shell | Resolution: 2.79→2.94 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.28 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4E36 Resolution: 2.789→10.994 Å / σ(F): 0.62 / Phase error: 31.58 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.057 Å2 / ksol: 0.311 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.789→10.994 Å
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Refine LS restraints |
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LS refinement shell |
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