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- PDB-3bvn: High resolution crystal structure of HLA-B*1402 in complex with t... -
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Basic information
Entry | Database: PDB / ID: 3bvn | ||||||
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Title | High resolution crystal structure of HLA-B*1402 in complex with the latent membrane protein 2 peptide (LMP2) of Epstein-Barr virus | ||||||
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![]() | IMMUNE SYSTEM / Major Histocompatibility Complex / MHC / Human Leukocyte Antigen / HLA / HLA-B14 / HLA-B*14 / HLA-B1402 / HLA-B*1402 / pLMP2 / Ankylosing Spondylitis / Disease mutation / Glycation / Glycoprotein / Immune response / Immunoglobulin domain / MHC I / Pyrrolidone carboxylic acid / Secreted / Alternative splicing / Cytoplasm / Host-virus interaction / Membrane / Phosphoprotein / Transmembrane / Ubl conjugation | ||||||
Function / homology | ![]() host cell endomembrane system / viral latency / 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 / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent ...host cell endomembrane system / viral latency / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / recycling endosome membrane / 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 / 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 / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / symbiont-mediated perturbation of host ubiquitin-like protein modification / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / host cell perinuclear region of cytoplasm / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Uchanska-Ziegler, B. / Ziegler, A. | ||||||
![]() | ![]() Title: Structural basis for T cell alloreactivity among three HLA-B14 and HLA-B27 antigens Authors: Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Merino, E. / Lopez de Castro, J.A. / Uchanska-Ziegler, B. / Ziegler, A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Expression, purification and preliminary X-ray crystallographic analysis of the human major histocompatibility antigen HLA-B*1402 in complex with a viral peptide and with a self-peptide Authors: Kumar, P. / Vahedi-Faridi, A. / Merino, E. / Lopez de Castro, J.A. / Volz, A. / Ziegler, A. / Saenger, W. / Uchanska-Ziegler, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 169.9 KB | Display | ![]() |
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PDB format | ![]() | 135.3 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3bp4C ![]() 3bp7C ![]() 3bxnC ![]() 1uxwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32172.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1303.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: peptide pLMP2 chemically synthesized / References: UniProt: P13285 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20-22%(w/v) PEG 20 000, 0.1 M HEPES buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 17, 2007 / Details: mirrors |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. all: 26731 / Num. obs: 26731 / % possible obs: 93.15 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Biso Wilson estimate: 48.11 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 8.87 |
Reflection shell | Resolution: 2.55→2.64 Å / % possible all: 76.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UXW Resolution: 2.55→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.55→50 Å
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Refine LS restraints |
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