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Yorodumi- PDB-4wc8: Heterogeneous dodecamer formed from macrocycles containing a sequ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wc8 | |||||||||
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Title | Heterogeneous dodecamer formed from macrocycles containing a sequence from beta-2-microglobulin(63-69). | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Heterogeneous dodecamer / hexamer / dimers | |||||||||
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 | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.908 Å | |||||||||
Authors | Spencer, R.K. / Nowick, J.S. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2015 Title: X-ray Crystallographic Structures of Oligomers of Peptides Derived from beta 2-Microglobulin. Authors: Spencer, R.K. / Kreutzer, A.G. / Salveson, P.J. / Li, H. / Nowick, J.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wc8.cif.gz | 132.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wc8.ent.gz | 115.7 KB | Display | PDB format |
PDBx/mmJSON format | 4wc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/4wc8 ftp://data.pdbj.org/pub/pdb/validation_reports/wc/4wc8 | HTTPS FTP |
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-Related structure data
Related structure data | 4p4vC 4p4wC 4p4xC 4p4yC 4p4zC 4x0sC 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 on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 1986.140 Da / Num. of mol.: 6 / Source method: obtained synthetically Details: this sequence occurs naturally in humans beta-2-microglobulin. Source: (synth.) synthetic construct (others) / References: UniProt: P61769*PLUS #2: Protein/peptide | Mass: 2028.219 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P61769*PLUS #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris, pH 7.5, 0.2 M Li2SO4, 30% PEG 400 / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2014 |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.908→31.59 Å / Num. all: 85498 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 26.16 Å2 / Rmerge(I) obs: 0.08446 / Net I/σ(I): 12.15 |
Reflection shell | Resolution: 1.908→1.976 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.5385 / Mean I/σ(I) obs: 2.61 / % possible all: 96.93 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD / Resolution: 1.908→31.588 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.74 / 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: 1.908→31.588 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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