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- PDB-6h6d: Crystal structures of the murine class I major histocompatibility... -
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Basic information
Entry | Database: PDB / ID: 6h6d | ||||||
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Title | Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with adenovirus-derived peptide Ad10 | ||||||
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![]() | IMMUNE SYSTEM / MHC class I / adenovirus | ||||||
Function / homology | ![]() regulation by virus of viral protein levels in host cell / positive regulation of protein sumoylation / molecular sequestering activity / 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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint ...regulation by virus of viral protein levels in host cell / positive regulation of protein sumoylation / molecular sequestering activity / 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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / 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 / regulation of protein localization / 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 / symbiont-mediated suppression of host gene expression / T cell differentiation in thymus / protein refolding / symbiont-mediated perturbation of host ubiquitin-like protein modification / protein homotetramerization / DNA-binding transcription factor binding / intracellular iron ion homeostasis / amyloid fibril formation / molecular adaptor activity / learning or memory / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / virus-mediated perturbation of host defense response / host cell nucleus / positive regulation of cell population proliferation / protein-containing complex binding / regulation of DNA-templated transcription / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Achour, A. / Sandalova, T. / Han, X. | ||||||
![]() | ![]() Title: Crystal structures of H-2Db and H-2Dbm13 with cancer-associated Ad 10 peptide reveal that subtle changes in the peptide environment impact thermostability and alloreactivity Authors: Han, X. / Abualrous, E.T. / Badia-Martines, D. / Sandalova, T. / Sun, R. / van Hall, T. / Ossendorp, F. / Achour, 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 | ![]() | 175.7 KB | Display | ![]() |
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PDB format | ![]() | 137.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489.2 KB | Display | ![]() |
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Full document | ![]() | 500.9 KB | Display | |
Data in XML | ![]() | 30.9 KB | Display | |
Data in CIF | ![]() | 42.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6h6hC ![]() 1n5aS 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: 38449.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11704.359 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: 998.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 4 types, 145 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1.8M ammonium sulphate, 0.1M Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→20 Å / Num. obs: 42622 / % possible obs: 90 % / Redundancy: 3.5 % / Rsym value: 0.137 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.34→2.5 Å / Rmerge(I) obs: 0.64 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1N5A Resolution: 2.4→19.98 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.822 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.235 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.314 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→19.98 Å
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Refine LS restraints |
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