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Open data
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Basic information
Entry | Database: PDB / ID: 4l8d | ||||||
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Title | Crystal structure of the H2Db in complex with the NP-N5D peptide | ||||||
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![]() | IMMUNE SYSTEM / Influenza / viral escape / T cell immunity | ||||||
Function / homology | ![]() Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / peptide binding / 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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Rossjohn, J. / Gras, S. | ||||||
![]() | ![]() Title: Acute emergence and reversion of influenza A virus quasispecies within CD8(+) T cell antigenic peptides. Authors: Valkenburg, S.A. / Quinones-Parra, S. / Gras, S. / Komadina, N. / McVernon, J. / Wang, Z. / Halim, H. / Iannello, P. / Cole, C. / Laurie, K. / Kelso, A. / Rossjohn, J. / Doherty, P.C. / ...Authors: Valkenburg, S.A. / Quinones-Parra, S. / Gras, S. / Komadina, N. / McVernon, J. / Wang, Z. / Halim, H. / Iannello, P. / Cole, C. / Laurie, K. / Kelso, A. / Rossjohn, J. / Doherty, P.C. / Turner, S.J. / Kedzierska, 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 | ![]() | 193.4 KB | Display | ![]() |
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PDB format | ![]() | 152.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4l8bC ![]() 4l8cC ![]() 4huuS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 32470.111 Da / Num. of mol.: 2 / Fragment: UNP residues 25-304 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein/peptide | Mass: 1027.084 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Sequence details | IN CHAINS B AND D, A85D (UNP A105D) IS A NATURAL VARIANT. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl, pH 8.5, 0.2 M lithium sulfate, 25-30% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→136.132 Å / Num. all: 74976 / Num. obs: 74976 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 26.7 Å2 / Rsym value: 0.126 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4HUU Resolution: 1.9→80.87 Å / Cor.coef. Fo:Fc: 0.9472 / Cor.coef. Fo:Fc free: 0.9254 / Occupancy max: 1 / Occupancy min: 0.03 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.157 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.135
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Displacement parameters | Biso mean: 31.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.218 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→80.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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