+Open data
-Basic information
Entry | Database: PDB / ID: 4l8b | ||||||
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Title | Crystal structure of the H2Db in complex with the NP-N5H peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Influenza / viral escape / T cell immunity | ||||||
Function / homology | Function and homology information 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 / 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 / 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 / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / 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 / lysosomal membrane / external side of plasma 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Rossjohn, J. / Gras, S. | ||||||
Citation | Journal: Nat Commun / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l8b.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l8b.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 4l8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l8b_validation.pdf.gz | 461.1 KB | Display | wwPDB validaton report |
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Full document | 4l8b_full_validation.pdf.gz | 466.2 KB | Display | |
Data in XML | 4l8b_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 4l8b_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/4l8b ftp://data.pdbj.org/pub/pdb/validation_reports/l8/4l8b | HTTPS FTP |
-Related structure data
Related structure data | 4l8cC 4l8dC 4huuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32470.111 Da / Num. of mol.: 1 / Fragment: UNP residues 25-304 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899 |
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#2: Protein | Mass: 11660.350 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1050.144 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 140 molecules
#4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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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: 3.13 Å3/Da / Density % sol: 60.66 % |
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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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.956 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 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: 2.2→45.495 Å / Num. all: 29420 / Num. obs: 29420 / % possible obs: 99.3 % / Redundancy: 7.1 % / Biso Wilson estimate: 52.43 Å2 / Rsym value: 0.064 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.804 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HUU Resolution: 2.2→45.49 Å / Cor.coef. Fo:Fc: 0.9485 / Cor.coef. Fo:Fc free: 0.9314 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.205 / SU Rfree Blow DPI: 0.296 / SU Rfree Cruickshank DPI: 0.173
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Displacement parameters | Biso max: 134.81 Å2 / Biso mean: 57.1889 Å2 / Biso min: 18.48 Å2
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Refine analyze | Luzzati coordinate error obs: 0.296 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→45.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Total num. of bins used: 15
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