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- PDB-6ryf: High-resolution crystal structure of ERAP1 in complex with 15mer ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ryf | |||||||||
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Title | High-resolution crystal structure of ERAP1 in complex with 15mer 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 / Synthesis and processing of ENV and VPU / evasion of host immune response / antigen processing and presentation of peptide antigen via MHC class I / metalloexopeptidase activity / Alpha-defensins / peptide catabolic process / regulation of innate immune response ...interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / Synthesis and processing of ENV and VPU / evasion of host immune response / antigen processing and presentation of peptide antigen via MHC class I / metalloexopeptidase activity / Alpha-defensins / peptide catabolic process / regulation of innate immune response / fat cell differentiation / Dectin-2 family / metalloaminopeptidase activity / membrane protein ectodomain proteolysis / Binding and entry of HIV virion / aminopeptidase activity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / response to bacterium / Assembly Of The HIV Virion / Budding and maturation of HIV virion / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / positive regulation of angiogenesis / angiogenesis / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / endopeptidase activity / viral protein processing / symbiont entry into host cell / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / endoplasmic reticulum membrane / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion 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 | ![]() | 391.4 KB | Display | ![]() |
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PDB format | ![]() | 317.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 40.8 KB | Display | |
Data in CIF | ![]() | 60.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rqxC ![]() 2yd0S C: citing same article ( 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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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AG
#1: Protein | Mass: 102208.523 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: 1767.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC PHOSPHINIC PSEUDOPEPTIDE / Source: (synth.) ![]() ![]() |
-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Sugar | |
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-Non-polymers , 6 types, 617 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PPI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PPI.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / | ||||||
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#5: Chemical | ChemComp-B3P / | ||||||
#6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-NA / #8: Chemical | ChemComp-PPI / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM propionic acid, cacodylate and Bis-tris propane pH 7.0, 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / 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: 1.72→91.52 Å / Num. obs: 106245 / % possible obs: 99.98 % / Redundancy: 8 % / CC1/2: 0.999 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.72→1.75 Å / Num. unique obs: 5264 / CC1/2: 0.368 / % possible all: 99.98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2YD0 Resolution: 1.72→91.52 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→91.52 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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