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- PDB-1bii: THE CRYSTAL STRUCTURE OF H-2DD MHC CLASS I IN COMPLEX WITH THE HI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bii | ||||||
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Title | THE CRYSTAL STRUCTURE OF H-2DD MHC CLASS I IN COMPLEX WITH THE HIV-1 DERIVED PEPTIDE P18-110 | ||||||
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![]() | COMPLEX (MHC I/PEPTIDE) / COMPLEX (MHC I-PEPTIDE) / MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I DD / TRANSMEMBRANE / GLYCOPROTEIN / COMPLEX (MHC I-PEPTIDE) complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Achour, A. / Persson, K. / Harris, R.A. / Sundback, J. / Sentman, C.L. / Lindqvist, Y. / Schneider, G. / Karre, K. | ||||||
![]() | ![]() Title: The crystal structure of H-2Dd MHC class I complexed with the HIV-1-derived peptide P18-I10 at 2.4 A resolution: implications for T cell and NK cell recognition. Authors: Achour, A. / Persson, K. / Harris, R.A. / Sundback, J. / Sentman, C.L. / Lindqvist, Y. / Schneider, G. / Karre, K. #1: ![]() Title: Murine Mhc Class I H-2Dd Complex: Expression, Refolding and Crystallisation Authors: Achour, A. / Harris, R.A. / Persson, K. / Sundback, J. / Sentman, C.L. / Schneider, G. / Lindqvist, Y. / Karre, 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 | ![]() | 89.8 KB | Display | ![]() |
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PDB format | ![]() | 70 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1vacS 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: 41162.340 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, EXTRACELLULAR DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 13840.981 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1075.265 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop / Details: Achour, A., (1998) Acta Cryst., D55, 260. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Oct 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.901 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. obs: 20963 / % possible obs: 96.5 % / Biso Wilson estimate: 60 Å2 / Rsym value: 0.04 / Net I/σ(I): 34 |
Reflection shell | Resolution: 2.4→2.46 Å / Mean I/σ(I) obs: 4.7 / Rsym value: 0.298 / % possible all: 94.6 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 199263 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 94.6 % / Rmerge(I) obs: 0.298 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1VAC Resolution: 2.4→6 Å
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Displacement parameters | Biso mean: 63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→6 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.293 / Rfactor Rfree: 0.338 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 6 Å / Rfactor Rfree: 0.323 / Rfactor obs: 0.278 |