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- PDB-2xfx: cattle MHC class I N01301 presenting an 11mer from Theileria parva -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xfx | ||||||
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Title | cattle MHC class I N01301 presenting an 11mer from Theileria parva | ||||||
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![]() | IMMUNE SYSTEM / MAJOR HISTOCOMPATIBILITY / EAST COAST FEVER / THEILERIOSIS | ||||||
Function / homology | ![]() ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / antigen processing and presentation / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / antigen processing and presentation / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / membrane => GO:0016020 / immune response / lysosomal membrane / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Macdonald, I.K. / Harkiolaki, M. / Hunt, L. / Morrison, W.I. / Connelley, T. / Graham, S.P. / Jones, E.Y. / Flower, D.R. / Ellis, S.A. | ||||||
![]() | ![]() Title: Mhc Class I Bound to an Immunodominant Theileria Parva Epitope Demonstrates Unconventional Presentation to T Cell Receptors. Authors: Macdonald, I.K. / Harkiolaki, M. / Hunt, L. / Connelley, T. / Carroll, A.V. / Machugh, N.D. / Graham, S.P. / Jones, E.Y. / Morrison, W.I. / Flower, D.R. / Ellis, S.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.2 KB | Display | ![]() |
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PDB format | ![]() | 138 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.2 KB | Display | ![]() |
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Full document | ![]() | 442.8 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1agfS 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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Unit cell |
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Components
#1: Protein | Mass: 32251.480 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-297 Source method: isolated from a genetically manipulated source Details: MHC CLASS I ALPHA CHAIN / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11724.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1294.558 Da / Num. of mol.: 1 / Fragment: 214-224 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.9 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 20% PEG 8000, 50MM POTASSIUM PHOSPHATE, PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 44056 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AGF Resolution: 1.9→45.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.667 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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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 mean: 22.304 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→45.51 Å
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Refine LS restraints |
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