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Yorodumi- PDB-5csb: The crystal structure of beta2-microglobulin D76N mutant at room ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5csb | ||||||
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Title | The crystal structure of beta2-microglobulin D76N mutant at room temperature | ||||||
Components | Beta-2-microglobulinBeta-2 microglobulin | ||||||
Keywords | IMMUNE SYSTEM / Beta-2 Microglobulin / amyloidosis / room temperature / Immunoglobulin-like | ||||||
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: 1.719 Å | ||||||
Authors | de Rosa, M. / Mota, C.S. / de Sanctis, D. / Bolognesi, M. / Ricagno, S. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity. Authors: Le Marchand, T. / de Rosa, M. / Salvi, N. / Sala, B.M. / Andreas, L.B. / Barbet-Massin, E. / Sormanni, P. / Barbiroli, A. / Porcari, R. / Sousa Mota, C. / de Sanctis, D. / Bolognesi, M. / ...Authors: Le Marchand, T. / de Rosa, M. / Salvi, N. / Sala, B.M. / Andreas, L.B. / Barbet-Massin, E. / Sormanni, P. / Barbiroli, A. / Porcari, R. / Sousa Mota, C. / de Sanctis, D. / Bolognesi, M. / Emsley, L. / Bellotti, V. / Blackledge, M. / Camilloni, C. / Pintacuda, G. / Ricagno, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5csb.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5csb.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 5csb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/5csb ftp://data.pdbj.org/pub/pdb/validation_reports/cs/5csb | HTTPS FTP |
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-Related structure data
Related structure data | 4rmuC 4rmvC 4rmwC 5cs7C 5csgC 4fxlS S: Starting model for refinement C: citing same article (ref.) |
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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
#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) / References: UniProt: P61769 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 30% PEG 4000, 0.1M sodium acetate, 15% glycerol, 0.2M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 293 K / Ambient temp details: room temperature |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.719→45.045 Å / Num. obs: 10186 / % possible obs: 92.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.719→1.81 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.2 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FXL Resolution: 1.719→45.045 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 23.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.719→45.045 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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