+Open data
-Basic information
Entry | Database: PDB / ID: 7mwc | ||||||
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Title | ERAP1 binds peptide C-terminus of a LPF sequence (AAAAFKARKF) | ||||||
Components | Endoplasmic reticulum aminopeptidase 1,LPF sequence | ||||||
Keywords | HYDROLASE / Antigen presentation / ERAP1 molecular ruler mechanism | ||||||
Function / homology | Function and homology information interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / 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 / metalloexopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / 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 / extracellular exosome / zinc ion binding / extracellular region / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Guo, H.C. / Sui, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Immunobiology / Year: 2021 Title: ERAP1 binds peptide C-termini of different sequences and/or lengths by a common recognition mechanism. Authors: Sui, L. / Guo, H.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mwc.cif.gz | 324.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mwc.ent.gz | 263.1 KB | Display | PDB format |
PDBx/mmJSON format | 7mwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/7mwc ftp://data.pdbj.org/pub/pdb/validation_reports/mw/7mwc | HTTPS FTP |
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-Related structure data
Related structure data | 7mwbC 3rjoS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 48952.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Some residues are missing or truncated to the beta carbon, due to poor local density Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others) Gene: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9NZ08, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases, EC: 3.4.1.1 #2: Water | ChemComp-HOH / | Sequence details | Residues 529-941 are ERAP1, and residues 942-951 constitute the LPF sequence | |
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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: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100mM Tris, pH 8.5, 12% w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→58.2 Å / Num. obs: 31557 / % possible obs: 90 % / Redundancy: 2.25 % / Rsym value: 0.061 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3→3.2 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4503 / Rsym value: 0.16 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RJO Resolution: 3→55.12 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.795 / SU B: 34.767 / SU ML: 0.623 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.69 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.47 Å2 / Biso mean: 51.57 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 3→55.12 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 4687 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3→3.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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