+Open data
-Basic information
Entry | Database: PDB / ID: 4fxl | ||||||
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Title | Crystal structure of the D76N Beta-2 Microglobulin mutant | ||||||
Components | Beta-2-microglobulinBeta-2 microglobulin | ||||||
Keywords | IMMUNE SYSTEM / immunoglobin / beta-sandwitch / amyloidosis / pathologic mutation / genetic disease / MHC class I | ||||||
Function / homology | Function and homology information 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...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 / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / 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 / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / 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 / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Ricagno, S. / Bellotti, V. / Pepys, M.B. / Stoppini, M. / Bolognesi, M. | ||||||
Citation | Journal: N.Engl.J.Med. / Year: 2012 Title: Hereditary systemic amyloidosis due to Asp76Asn variant beta-2-microglobulin. Authors: Valleix, S. / Gillmore, J.D. / Bridoux, F. / Mangione, P.P. / Dogan, A. / Nedelec, B. / Boimard, M. / Touchard, G. / Goujon, J.M. / Lacombe, C. / Lozeron, P. / Adams, D. / Lacroix, C. / ...Authors: Valleix, S. / Gillmore, J.D. / Bridoux, F. / Mangione, P.P. / Dogan, A. / Nedelec, B. / Boimard, M. / Touchard, G. / Goujon, J.M. / Lacombe, C. / Lozeron, P. / Adams, D. / Lacroix, C. / Maisonobe, T. / Plante-Bordeneuve, V. / Vrana, J.A. / Theis, J.D. / Giorgetti, S. / Porcari, R. / Ricagno, S. / Bolognesi, M. / Stoppini, M. / Delpech, M. / Pepys, M.B. / Hawkins, P.N. / Bellotti, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fxl.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fxl.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/4fxl ftp://data.pdbj.org/pub/pdb/validation_reports/fx/4fxl | HTTPS FTP |
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-Related structure data
Related structure data | 1ldsS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11878.372 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 / Mutation: D76N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769 |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-PEG / |
#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: 1.91 Å3/Da / Density % sol: 35.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 18-20% PEG 4000, 20% glycerol, 0.2M ammonium acetate, 0.1 M MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 23, 2011 / Details: Toroidal Zerodur mirror |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→18.8 Å / Num. obs: 17632 / % possible obs: 98.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2542 / Rsym value: 0.375 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LDS Resolution: 1.4→18.8 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.012 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.763 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→18.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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