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- PDB-6rqx: High-resolution crystal structure of ERAP1 in complex with 10mer ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rqx | |||||||||
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Title | High-resolution crystal structure of ERAP1 in complex with 10mer phosphinic peptide | |||||||||
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![]() | HYDROLASE / endoplasmic reticulum aminopeptidase 1 / ERAP1 / antigen presentation | |||||||||
Function / homology | ![]() interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / metalloexopeptidase activity / peptide catabolic process / regulation of innate immune response / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis ...interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / metalloexopeptidase activity / peptide catabolic process / regulation of innate immune response / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis / aminopeptidase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / response to bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / positive regulation of angiogenesis / angiogenesis / endopeptidase activity / adaptive immune response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Giastas, P. / Stratikos, E. | |||||||||
![]() | ![]() Title: Mechanism for antigenic peptide selection by endoplasmic reticulum aminopeptidase 1. Authors: Giastas, P. / Mpakali, A. / Papakyriakou, A. / Lelis, A. / Kokkala, P. / Neu, M. / Rowland, P. / Liddle, J. / Georgiadis, D. / Stratikos, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 397.5 KB | Display | ![]() |
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PDB format | ![]() | 324.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 42.2 KB | Display | |
Data in CIF | ![]() | 64.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ryfC ![]() 6q4rS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 106939.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: Q9NZ08, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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#2: Protein/peptide | Mass: 1298.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: phosphinic peptide, antigenic epitope / Source: (synth.) ![]() |
-Sugars , 4 types, 4 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-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 |
#5: 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 |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 777 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-ZN / | ||||||||
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#8: Chemical | ChemComp-SCN / #9: Chemical | ChemComp-EDO / #10: Chemical | ChemComp-NA / #11: Chemical | #12: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.38 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 200 mM potassium thiocyanate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→73.75 Å / Num. obs: 114099 / % possible obs: 99.71 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09287 / Net I/σ(I): 12.11 |
Reflection shell | Resolution: 1.68→1.742 Å / Redundancy: 5.3 % / Num. unique obs: 11316 / % possible all: 99.78 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6Q4R Resolution: 1.68→73.681 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→73.681 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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