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Yorodumi- PDB-2cii: The crystal structure of H-2Db complexed with a partial peptide e... -
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-Basic information
Entry | Database: PDB / ID: 2cii | ||||||
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Title | The crystal structure of H-2Db complexed with a partial peptide epitope suggests an MHC Class I assembly-intermediate | ||||||
Components |
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Keywords | IMMUNE SYSTEM/PEPTIDE / COMPLEX (ANTIGEN-PEPTIDE) / MHC CLASS I / PEPTIDE BINDING / SENDAI VIRUS / IMMUNE RESPONSE / IMMUNOGLOBULIN DOMAIN / MHC I / PYRROLIDONE CARBOXYLIC ACID / GLYCOPROTEIN / MEMBRANE / TRANSMEMBRANE / IMMUNE SYSTEM-PEPTIDE complex | ||||||
Function / homology | Function and homology information helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding ...helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / ER-Phagosome pathway / iron ion transport / early endosome membrane / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) HUMAN PARAINFLUENZA 1 VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Glithero, A. / Tormo, J. / Doering, K. / Kojima, M. / Jones, E.Y. / Elliott, T. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2006 Title: The crystal structure of H-2D(b) complexed with a partial peptide epitope suggests a major histocompatibility complex class I assembly intermediate. Authors: Glithero, A. / Tormo, J. / Doering, K. / Kojima, M. / Jones, E.Y. / Elliott, T. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cii.cif.gz | 97.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cii.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 2cii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cii_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 2cii_full_validation.pdf.gz | 461.9 KB | Display | |
Data in XML | 2cii_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 2cii_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/2cii ftp://data.pdbj.org/pub/pdb/validation_reports/ci/2cii | HTTPS FTP |
-Related structure data
Related structure data | 1ce6S 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: 31933.535 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P01899 | ||||
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P61769 | ||||
#3: Protein/peptide | Mass: 949.060 Da / Num. of mol.: 1 / Fragment: RESIDUES 324-332 / Source method: obtained synthetically / Source: (synth.) HUMAN PARAINFLUENZA 1 VIRUS / References: UniProt: P26590 | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | INVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM BETA-2-MICROGLOBULIN IS THE ...INVOLVED IN THE PRESENTATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57 % |
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Crystal grow | pH: 5 Details: 25% PEG 6000, 100MM AMMONIUM SULFATE, 100 MM SODIUM CHLORIDE, 50 MM MES PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. obs: 15880 / % possible obs: 95.8 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.55→2.61 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 5.3 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CE6 Resolution: 2.55→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 30.0534 Å2 / ksol: 0.349682 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.545 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.64 Å / Total num. of bins used: 10
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Xplor file |
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