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Open data
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Basic information
Entry | Database: PDB / ID: 5eu4 | ||||||
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Title | HLA Class I antigen | ||||||
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![]() | IMMUNE SYSTEM / IMMUNO / HLA-A02 / 1E6-TCR / Cross-reactivity | ||||||
Function / homology | ![]() cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome membrane / multivesicular body, internal vesicle / melanosome organization / multivesicular body membrane / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding ...cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome membrane / multivesicular body, internal vesicle / melanosome organization / multivesicular body membrane / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / melanosome / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Rizkallah, P.J. / Bianchi, V. / Cole, D.K. / Sewell, A.K. | ||||||
![]() | ![]() Title: A Molecular Switch Abrogates Glycoprotein 100 (gp100) T-cell Receptor (TCR) Targeting of a Human Melanoma Antigen. Authors: Bianchi, V. / Bulek, A. / Fuller, A. / Lloyd, A. / Attaf, M. / Rizkallah, P.J. / Dolton, G. / Sewell, A.K. / Cole, D.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 333 KB | Display | ![]() |
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PDB format | ![]() | 271.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496 KB | Display | ![]() |
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Full document | ![]() | 507.8 KB | Display | |
Data in XML | ![]() | 31.8 KB | Display | |
Data in CIF | ![]() | 45 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5eu3C ![]() 5eu5C ![]() 5eu6C ![]() 4i4wS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 888.018 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) / References: UniProt: P40967*PLUS |
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-Non-polymers , 4 types, 251 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / | ||||
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#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.55 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.0, 15 % Glycerol, 20 % PEG 4000 / PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 24, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.12→43.39 Å / Num. obs: 49667 / % possible obs: 97.4 % / Redundancy: 2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.084 / Net I/σ(I): 6.5 / Num. measured all: 99386 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4I4W Resolution: 2.12→43.39 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2163 / WRfactor Rwork: 0.1735 / FOM work R set: 0.8231 / SU B: 11.854 / SU ML: 0.147 / SU R Cruickshank DPI: 0.2117 / SU Rfree: 0.1722 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 115.43 Å2 / Biso mean: 34.769 Å2 / Biso min: 16.88 Å2
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Refinement step | Cycle: final / Resolution: 2.12→43.39 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.12→2.175 Å / Total num. of bins used: 20
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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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