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Open data
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Basic information
Entry | Database: PDB / ID: 1jnj | ||||||
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Title | NMR solution structure of the human beta2-microglobulin | ||||||
![]() | beta2-microglobulin | ||||||
![]() | IMMUNE SYSTEM / immunoglobulin constant domain | ||||||
Function / homology | ![]() 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...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 / 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 / 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 / positive regulation of cellular senescence / peptide antigen binding / 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 / 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 / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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 | SOLUTION NMR / simulated annealing, restrained molecular dynamics, restrained molecular mechanics | ||||||
![]() | Verdone, G. / Corazza, A. / Viglino, P. / Pettirossi, F. / Giorgetti, S. / Mangione, P. / Andreola, A. / Stoppini, M. / Bellotti, V. / Esposito, G. | ||||||
![]() | ![]() Title: The solution structure of human beta2-microglobulin reveals the prodromes of its amyloid transition. Authors: Verdone, G. / Corazza, A. / Viglino, P. / Pettirossi, F. / Giorgetti, S. / Mangione, P. / Andreola, A. / Stoppini, M. / Bellotti, V. / Esposito, G. #1: ![]() Title: Removal of the N-terminal hexapeptide from human beta2-microglobulin facilitates protein aggregation and fibril formation Authors: Esposito, G. / Michelutti, R. / Verdone, G. / Viglino, P. / Hernandez, H. / Robinson, C.V. / Amoresano, A. / Dal Piaz, F. / Monti, M. / Pucci, P. / Mangione, P. / Stoppini, M. / Merlini, G. ...Authors: Esposito, G. / Michelutti, R. / Verdone, G. / Viglino, P. / Hernandez, H. / Robinson, C.V. / Amoresano, A. / Dal Piaz, F. / Monti, M. / Pucci, P. / Mangione, P. / Stoppini, M. / Merlini, G. / Ferri, G. / Bellotti, V. #2: ![]() Title: Beta2-microglobulin can be refolded into a native state from ex vivo amyloid fibrils. Authors: Bellotti, V. / Stoppini, M. / Mangione, P. / Sunde, M. / Robinson, C.V. / Asti, L. / Brancaccio, D. / Ferri, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 637.2 KB | Display | ![]() |
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PDB format | ![]() | 554.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 356.4 KB | Display | ![]() |
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Full document | ![]() | 471 KB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques |
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Sample preparation
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
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Processing
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Refinement | Method: simulated annealing, restrained molecular dynamics, restrained molecular mechanics Software ordinal: 1 Details: the structures are based on a total of 1608 restraints, 1541 are NOE-derived distance contraints, 67 dihedral angle restraints | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 380 / Conformers submitted total number: 20 |