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Yorodumi- PDB-2vaa: MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vaa | |||||||||
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Title | MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND VESICULAR STOMATITIS VIRUS NUCLEOPROTEIN | |||||||||
Components |
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Keywords | COMPLEX (MHC I/PEPTIDE) / HISTOCOMPATIBILITY ANTIGEN / CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX / MHC I / MHC-PEPTIDE COMPLEX / COMPLEX (MHC I-PEPTIDE) COMPLEX | |||||||||
Function / homology | Function and homology information 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 / helical viral capsid / 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 ...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 / helical viral capsid / 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 / Neutrophil degranulation / peptide 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(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 / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / learning or memory / defense response to bacterium / ribonucleoprotein complex / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Vesicular stomatitis virus | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | |||||||||
Authors | Fremont, D.H. / Wilson, I.A. | |||||||||
Citation | Journal: Science / Year: 1992 Title: Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb. Authors: Fremont, D.H. / Matsumura, M. / Stura, E.A. / Peterson, P.A. / Wilson, I.A. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: Crystal Structure of an H-2Kb-Ovalbumin Peptide Complex Reveals the Interplay of Primary and Secondary Anchor Positions in the Major Histocompatibility Complex Binding Groove Authors: Fremont, D.H. / Stura, E.A. / Matsumura, M. / Peterson, P.A. / Wilson, I.A. #2: Journal: Science / Year: 1992 Title: Emerging Principles for the Recognition of Peptide Antigens by Mhc Class I Molecules Authors: Matsumura, M. / Fremont, D.H. / Peterson, P.A. / Wilson, I.A. #3: Journal: J.Mol.Biol. / Year: 1992 Title: Crystallization of Murine Major Histocompatibility Complex Class I H-2Kb with Single Peptides Authors: Stura, E.A. / Matsumura, M. / Fremont, D.H. / Saito, Y. / Peterson, P.A. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vaa.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vaa.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vaa_validation.pdf.gz | 373.8 KB | Display | wwPDB validaton report |
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Full document | 2vaa_full_validation.pdf.gz | 377 KB | Display | |
Data in XML | 2vaa_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 2vaa_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/2vaa ftp://data.pdbj.org/pub/pdb/validation_reports/va/2vaa | HTTPS FTP |
-Related 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: 31648.322 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/B / Gene: BETA-2-MICROGLOBULIN / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01901 |
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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) / Strain: BALB/B / Gene: BETA-2-MICROGLOBULIN / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887 |
#3: Protein/peptide | Mass: 956.078 Da / Num. of mol.: 1 / Fragment: RESIDUES 52 - 59 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vesicular stomatitis virus / Genus: Vesiculovirus / References: UniProt: P11212 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.13 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 22.5 ℃ / pH: 6.25 / Method: vapor diffusion, sitting drop / Details: used to seeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: XENTRONICS / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 23289 / % possible obs: 90 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.079 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. measured all: 81010 |
-Processing
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Refinement | Resolution: 2.3→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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