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- PDB-8e13: Structures of HLA-B8E76C loaded with long peptides reveal novel f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 80000000000000 | ||||||
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Title | Structures of HLA-B8E76C loaded with long peptides reveal novel features at the N-terminus of the groove | ||||||
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Function / homology | ![]() positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Li, L. / Bouvier, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of MHC class I complexes reveal the elusive intermediate conformations explored during peptide editing. Authors: Li, L. / Peng, X. / Batliwala, M. / Bouvier, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.5 KB | Display | ![]() |
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PDB format | ![]() | 141.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8e2zC ![]() 8e8iC ![]() 8ec5C ![]() 6p2sS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31902.004 Da / Num. of mol.: 1 / Mutation: E76C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1003.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.49 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion / pH: 5.6 Details: 0.2 M ammonium acetate, 18% PEG 4000, 0.1 M sodium citrate, |
-Data collection
Diffraction | Mean temperature: 103 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.37→65.47 Å / Num. obs: 95762 / % possible obs: 99.5 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.37→1.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.48 / Num. unique obs: 4263 / % possible all: 97 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 6P2S Resolution: 1.37→27 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.194 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.057 / 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: 116.15 Å2 / Biso mean: 18.537 Å2 / Biso min: 7.19 Å2
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Refinement step | Cycle: final / Resolution: 1.37→27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.37→1.406 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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