+Open data
-Basic information
Entry | Database: PDB / ID: 2z9t | ||||||
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Title | Crystal structure of the human beta-2 microglobulin mutant W60G | ||||||
Components | Beta-2-microglobulinBeta-2 microglobulin | ||||||
Keywords | IMMUNE SYSTEM / beta-2-microglobulin / tryptophan / glycine / amyloidosis / DRA / beta fibrils / Disease mutation / Glycation / Glycoprotein / Immune response / Immunoglobulin domain / MHC I / Pyrrolidone carboxylic acid / Secreted | ||||||
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: 1.8 Å | ||||||
Authors | Ricagno, S. / Bolognesi, M. / Bellotti, V. / Corazza, A. / Rennella, E. / Gural, D. / Mimmi, M.C. / Betto, E. / Pucillo, C. / Fogolari, F. ...Ricagno, S. / Bolognesi, M. / Bellotti, V. / Corazza, A. / Rennella, E. / Gural, D. / Mimmi, M.C. / Betto, E. / Pucillo, C. / Fogolari, F. / Viglino, P. / Raimondi, S. / Giorgetti, S. / Bolognesi, B. / Merlini, G. / Stoppini, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: The controlling roles of Trp60 and Trp95 in beta2-microglobulin function, folding and amyloid aggregation properties Authors: Esposito, G. / Ricagno, S. / Corazza, A. / Rennella, E. / Gumral, D. / Mimmi, M.C. / Betto, E. / Pucillo, C.E.M. / Fogolari, F. / Viglino, P. / Raimondi, S. / Giorgetti, S. / Bolognesi, B. / ...Authors: Esposito, G. / Ricagno, S. / Corazza, A. / Rennella, E. / Gumral, D. / Mimmi, M.C. / Betto, E. / Pucillo, C.E.M. / Fogolari, F. / Viglino, P. / Raimondi, S. / Giorgetti, S. / Bolognesi, B. / Merlini, G. / Stoppini, M. / Bolognesi, M. / Bellotti, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z9t.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z9t.ent.gz | 25.9 KB | Display | PDB format |
PDBx/mmJSON format | 2z9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/2z9t ftp://data.pdbj.org/pub/pdb/validation_reports/z9/2z9t | HTTPS FTP |
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-Related structure data
Related structure data | 2vb5C 1py4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 11750.198 Da / Num. of mol.: 1 / Mutation: W60G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NM_004048 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P61769 |
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#2: 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: 2.32 Å3/Da / Density % sol: 46.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES, PEG 4000, Ammonium acetate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 6, 2007 |
Radiation | Monochromator: Diamond (111) / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.2 Å / Num. all: 9273 / Num. obs: 9273 / % possible obs: 93.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 13.3 Å2 / Rsym value: 0.068 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 8 / Num. unique all: 1375 / Rsym value: 0.112 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PY4 Resolution: 1.8→19.16 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.569 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.143 / ESU R Free: 0.133 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Rfactor Rfree error: 0.227 / 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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