+Open data
-Basic information
Entry | Database: PDB / ID: 2x89 | ||||||
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Title | Structure of the Beta2_microglobulin involved in amyloidogenesis | ||||||
Components |
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Keywords | IMMUNE SYSTEM | ||||||
Function / homology | Function and homology information immunoglobulin complex / immunoglobulin mediated immune response / 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 / antigen binding ...immunoglobulin complex / immunoglobulin mediated immune response / 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 / antigen 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / 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 / blood microparticle / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal 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 / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | CAMELUS DROMEDARIUS (Arabian camel) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å | ||||||
Authors | Domanska, K. / Srinivasan, V. / Vanderhaegen, S. / Pardon, E. / Marquez, J.A. / Bellotti, V. / Wyns, L. / Steyaert, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Atomic Structure of a Nanobody-Trapped Domain-Swapped Dimer of an Amyloidogenic {Beta}2-Microglobulin Variant. Authors: Domanska, K. / Vanderhaegen, S. / Srinivasan, V. / Pardon, E. / Dupeux, F. / Marquez, J.A. / Giorgetti, S. / Stoppini, M. / Wyns, L. / Bellotti, V. / Steyaert, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x89.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x89.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 2x89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/2x89 ftp://data.pdbj.org/pub/pdb/validation_reports/x8/2x89 | HTTPS FTP |
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-Related structure data
Related structure data | 1bmgS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Antibody | Mass: 14162.595 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CAMELUS DROMEDARIUS (Arabian camel) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A2KD59*PLUS #2: Protein | Mass: 11153.478 Da / Num. of mol.: 4 / Fragment: RESIDUES 27-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61769 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.7 % / Description: NONE |
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Crystal grow | Details: 6%PEG4000, 0.2M AMMONIUM SULPHATE, 0.1M NA-ACETEATE PH4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97812 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97812 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→20 Å / Num. obs: 66127 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.16→2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.1 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: PDB ENTRY 1BMG Resolution: 2.16→19.85 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.727 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.186 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONE MOLECULE IN THE ASYMMETRIC UNIT IS DISORDERED.
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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: 60.626 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→19.85 Å
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Refine LS restraints |
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