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Open data
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Basic information
Entry | Database: PDB / ID: 1bqh | |||||||||
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Title | MURINE CD8AA ECTODOMAIN FRAGMENT IN COMPLEX WITH H-2KB/VSV8 | |||||||||
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![]() | IMMUNE SYSTEM / T-CELL / CORECEPTOR / GLYCOPROTEIN / COMPLEX / IMMUNOLOGY / ANTIGEN | |||||||||
Function / homology | ![]() cytotoxic T cell differentiation / T cell mediated immunity / 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 exogenous peptide antigen via MHC class I / inner ear development ...cytotoxic T cell differentiation / T cell mediated immunity / 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 exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / positive regulation of calcium-mediated signaling / T cell activation / 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 / calcium-mediated signaling / 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 / T cell receptor signaling pathway / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / defense response to virus / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / receptor complex / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / protein kinase binding / structural molecule activity / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, J.H. / Reinherz, E.L. / Kern, P.S. / Chang, H.C. | |||||||||
![]() | ![]() Title: Structural basis of CD8 coreceptor function revealed by crystallographic analysis of a murine CD8alphaalpha ectodomain fragment in complex with H-2Kb. Authors: Kern, P.S. / Teng, M.K. / Smolyar, A. / Liu, J.H. / Liu, J. / Hussey, R.E. / Spoerl, R. / Chang, H.C. / Reinherz, E.L. / Wang, J.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 260.2 KB | Display | ![]() |
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PDB format | ![]() | 209.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 523 KB | Display | ![]() |
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Full document | ![]() | 599.1 KB | Display | |
Data in XML | ![]() | 54.6 KB | Display | |
Data in CIF | ![]() | 73.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vaaS 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: 31648.322 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: BETA CHAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein/peptide | Mass: 956.078 Da / Num. of mol.: 2 / Fragment: ANTIGENIC PEPTIDE / Source method: obtained synthetically #4: Protein | Mass: 14512.637 Da / Num. of mol.: 4 / Fragment: IG ECTODOMAIN FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: GENE FUSED TO THROMBIN CLEAVAGE SITE AND LEUCINE ZIPPER Cell line (production host): CHO LEC 3.2.8.1 / Gene (production host): CD8A / Production host: ![]() ![]() #5: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: 20-25% PEG 4K, 0.2M LI2SO4, 0.1M TRIS PH8.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS / Detector: CCD / Date: Apr 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→15 Å / Num. obs: 34131 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rsym value: 0.061 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.249 / % possible all: 90.7 |
Reflection | *PLUS Num. measured all: 99259 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 90.7 % / Rmerge(I) obs: 0.249 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VAA Resolution: 2.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 10.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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