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Yorodumi- PDB-1k8d: crystal structure of the non-classical MHC class Ib Qa-2 complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k8d | ||||||
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Title | crystal structure of the non-classical MHC class Ib Qa-2 complexed with a self peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / non-classical MHC class I / antigen presentation / preimplantation embryo devolepment gene product / Qa-2 / Q9 | ||||||
Function / homology | Function and homology information L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Major pathway of rRNA processing in the nucleolus and cytosol / 5.8S rRNA binding / : / Formation of a pool of free 40S subunits ...L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Major pathway of rRNA processing in the nucleolus and cytosol / 5.8S rRNA binding / : / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / antigen processing and presentation of peptide antigen via MHC class I / 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 / regulation of membrane depolarization / TAP complex binding / Golgi medial cisterna / CD8 receptor binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / embryo implantation / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / Neutrophil degranulation / T cell receptor binding / cytosolic ribosome / : / liver regeneration / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / cellular response to type II interferon / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / large ribosomal subunit rRNA binding / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / cytosolic large ribosomal subunit / cytoplasmic translation / antibacterial humoral response / iron ion transport / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / structural constituent of ribosome / defense response to Gram-positive bacterium / translation / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / synapse / protein-containing complex binding / nucleolus / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | He, X. / Tabaczewski, P. / Ho, J. / Stroynowski, I. / Garcia, K.C. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Promiscuous antigen presentation by the nonclassical MHC Ib Qa-2 is enabled by a shallow, hydrophobic groove and self-stabilized peptide conformation. Authors: He, X. / Tabaczewski, P. / Ho, J. / Stroynowski, I. / Garcia, K.C. | ||||||
History |
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Remark 999 | SEQUENCE THE CONFLICT IS BECAUSE THE STRUCTURE IS OF THE Q9 ALLELE OF QA-2, WHICH IS GLU AT THIS ...SEQUENCE THE CONFLICT IS BECAUSE THE STRUCTURE IS OF THE Q9 ALLELE OF QA-2, WHICH IS GLU AT THIS POSITION. THE P14429 REFERENCE IS FOR THE SEQUENCE OF THE Q7 ALLELE OF QA-2, WHICH IS GLN AT THIS POSITION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k8d.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k8d.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 1k8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/1k8d ftp://data.pdbj.org/pub/pdb/validation_reports/k8/1k8d | 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 |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31628.252 Da / Num. of mol.: 1 Fragment: EXTRACELLULAR ALPHA-1, EXTRACELLULAR ALPHA-2, EXTRACELLULAR ALPHA-3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Q9 / Production host: Escherichia coli (E. coli) / References: UniProt: P14429 |
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#2: Protein | Mass: 11704.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01887 |
#3: Protein/peptide | Mass: 1136.429 Da / Num. of mol.: 1 / Fragment: residues 137-145 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (mouse). References: UniProt: P14118, UniProt: P84099*PLUS |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.74 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG6000, HEPES, sodium chloride, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.08 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 16467 / Num. obs: 16467 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.112 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.37 / % possible all: 99 |
Reflection | *PLUS Lowest resolution: 60 Å / Num. measured all: 61755 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 99 % / Rmerge(I) obs: 0.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VAC Resolution: 2.3→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 30.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.043
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 60 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.2 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.365 / Rfactor Rwork: 0.285 / Rfactor obs: 0.285 |