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Yorodumi- PDB-1kg0: Structure of the Epstein-Barr Virus gp42 Protein Bound to the MHC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kg0 | ||||||
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Title | Structure of the Epstein-Barr Virus gp42 Protein Bound to the MHC class II Receptor HLA-DR1 | ||||||
Components |
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Keywords | Viral protein/Immune system / virus / c-type lectin domain / membrane fusion / MHC / Viral protein-Immune system COMPLEX | ||||||
Function / homology | Function and homology information regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / host cell membrane / PD-1 signaling / epidermis development / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / viral budding from plasma membrane / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / host cell surface receptor binding / immune response / positive regulation of protein phosphorylation / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / Golgi membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human herpesvirus 4 (Epstein-Barr virus) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Mullen, M.M. / Haan, K.M. / Longnecker, R. / Jardetzky, T.S. | ||||||
Citation | Journal: Mol.Cell / Year: 2002 Title: Structure of the Epstein-Barr virus gp42 protein bound to the MHC class II receptor HLA-DR1. Authors: Mullen, M.M. / Haan, K.M. / Longnecker, R. / Jardetzky, T.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kg0.cif.gz | 131 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kg0.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/1kg0 ftp://data.pdbj.org/pub/pdb/validation_reports/kg/1kg0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20913.568 Da / Num. of mol.: 1 / Fragment: ALPHA CHAIN, EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01903 |
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#2: Protein | Mass: 21908.523 Da / Num. of mol.: 1 / Fragment: BETA CHAIN, EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04229, UniProt: P01911*PLUS |
#3: Protein/peptide | Mass: 1506.807 Da / Num. of mol.: 1 / Fragment: Antigenic Peptide / Source method: obtained synthetically Details: Synthetic peptide derived from influenza hemagglutinin sequence Source: (synth.) synthetic construct (others) / References: UniProt: P03437*PLUS |
#4: Protein | Mass: 15631.763 Da / Num. of mol.: 1 / Fragment: Extracellular Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus) Genus: Lymphocryptovirus / Strain: GD1 / Plasmid: pBAC-gus3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03205 |
#5: 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: 3.53 Å3/Da / Density % sol: 65.13 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, Ammonium Acetate, Sodium Chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 27 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 101 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 25, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→30 Å / Num. all: 25595 / Num. obs: 25186 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 67 Å2 |
Reflection shell | Resolution: 2.65→2.82 Å / % possible all: 99.1 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 181993 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 99.1 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 4.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.65→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor obs: 0.221 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |