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Yorodumi- PDB-3myz: Protein induced photophysical changes to the amyloid indicator dy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3myz | ||||||
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Title | Protein induced photophysical changes to the amyloid indicator dye, thioflavin T | ||||||
Components | Beta-2-microglobulinBeta-2 microglobulin | ||||||
Keywords | IMMUNE SYSTEM / amyloid / Thioflavin T / Parkinson's / Alzheimer's / beta-2 microglobulin | ||||||
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 / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / 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: 1.6 Å | ||||||
Authors | Wolfe, L.S. / Calabrese, M.F. / Nath, A. / Blaho, D.V. / Miranker, A.D. / Xiong, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Protein-induced photophysical changes to the amyloid indicator dye thioflavin T. Authors: Wolfe, L.S. / Calabrese, M.F. / Nath, A. / Blaho, D.V. / Miranker, A.D. / Xiong, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3myz.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3myz.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 3myz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/3myz ftp://data.pdbj.org/pub/pdb/validation_reports/my/3myz | HTTPS FTP |
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-Related structure data
Related structure data | 3mztC 1kprS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 11888.383 Da / Num. of mol.: 2 / Mutation: H13F 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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-Non-polymers , 5 types, 168 molecules
#2: Chemical | ChemComp-HG / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-TLA / | #5: Chemical | #6: 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: 2.17 Å3/Da / Density % sol: 43.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG 3350, 50mM diammonium tartrate, 5mM Thioflavin T, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 38793 / % possible obs: 98.3 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 8.89 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.83 Å / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KPR Resolution: 1.6→29.27 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.46 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.098 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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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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