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Yorodumi- EMDB-2366: Electron cryo-microscopy of phosphorylation-mimicking mutants of ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2366 | |||||||||
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Title | Electron cryo-microscopy of phosphorylation-mimicking mutants of alphaB-crystallin: the hexamer | |||||||||
Map data | C3 reconstruction of hexameric alphaB phosphorylation mutants | |||||||||
Sample |
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Keywords | cryo electron microscopy / small heat shock protein / phosphorylation | |||||||||
Function / homology | Function and homology information microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / cardiac myofibril / regulation of programmed cell death / tubulin complex assembly / structural constituent of eye lens / negative regulation of amyloid fibril formation / M band / lens development in camera-type eye ...microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / cardiac myofibril / regulation of programmed cell death / tubulin complex assembly / structural constituent of eye lens / negative regulation of amyloid fibril formation / M band / lens development in camera-type eye / muscle organ development / actin filament bundle / HSF1-dependent transactivation / negative regulation of reactive oxygen species metabolic process / negative regulation of protein-containing complex assembly / muscle contraction / stress-activated MAPK cascade / synaptic membrane / response to hydrogen peroxide / negative regulation of cell growth / cellular response to gamma radiation / Z disc / unfolded protein binding / protein folding / response to estradiol / amyloid-beta binding / protein refolding / response to heat / microtubule binding / perikaryon / dendritic spine / lysosome / response to hypoxia / protein stabilization / axon / negative regulation of gene expression / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / protein-containing complex binding / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 17.0 Å | |||||||||
Authors | Peschek J / Braun N / Rohrberg J / Back K / Kriehuber T / Kastenmueller A / Weinkauf S / Buchner J | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2013 Title: Regulated structural transitions unleash the chaperone activity of αB-crystallin. Authors: Jirka Peschek / Nathalie Braun / Julia Rohrberg / Katrin Christiane Back / Thomas Kriehuber / Andreas Kastenmüller / Sevil Weinkauf / Johannes Buchner / Abstract: The small heat shock protein αB-crystallin is an oligomeric molecular chaperone that binds aggregation-prone proteins. As a component of the proteostasis system, it is associated with cataract, ...The small heat shock protein αB-crystallin is an oligomeric molecular chaperone that binds aggregation-prone proteins. As a component of the proteostasis system, it is associated with cataract, neurodegenerative diseases, and myopathies. The structural determinants for the regulation of its chaperone function are still largely elusive. Combining different experimental approaches, we show that phosphorylation-induced destabilization of intersubunit interactions mediated by the N-terminal domain (NTD) results in the remodeling of the oligomer ensemble with an increase in smaller, activated species, predominantly 12-mers and 6-mers. Their 3D structures determined by cryo-electron microscopy and biochemical analyses reveal that the NTD in these species gains flexibility and solvent accessibility. These modulated properties are accompanied by an increase in chaperone activity in vivo and in vitro and a more efficient cooperation with the heat shock protein 70 system in client folding. Thus, the modulation of the structural flexibility of the NTD, as described here for phosphorylation, appears to regulate the chaperone activity of αB-crystallin rendering the NTD a conformational sensor for nonnative proteins. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2366.map.gz | 1.6 MB | EMDB map data format | |
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Header (meta data) | emd-2366-v30.xml emd-2366.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | EMD-2366.png | 78.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2366 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2366 | HTTPS FTP |
-Validation report
Summary document | emd_2366_validation.pdf.gz | 187.2 KB | Display | EMDB validaton report |
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Full document | emd_2366_full_validation.pdf.gz | 186.3 KB | Display | |
Data in XML | emd_2366_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2366 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2366 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2366.map.gz / Format: CCP4 / Size: 4.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | C3 reconstruction of hexameric alphaB phosphorylation mutants | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Hexameric phosphorylation-mimicking mutant of alphaB-crystallin
Entire | Name: Hexameric phosphorylation-mimicking mutant of alphaB-crystallin |
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Components |
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-Supramolecule #1000: Hexameric phosphorylation-mimicking mutant of alphaB-crystallin
Supramolecule | Name: Hexameric phosphorylation-mimicking mutant of alphaB-crystallin type: sample / ID: 1000 / Details: The sample was polydisperse / Oligomeric state: Hexameric / Number unique components: 1 |
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Molecular weight | Theoretical: 121 KDa |
-Macromolecule #1: Hexameric phosphorylation-mimicking mutant of human alphaB-crystallin
Macromolecule | Name: Hexameric phosphorylation-mimicking mutant of human alphaB-crystallin type: protein_or_peptide / ID: 1 Name.synonym: Alpha(B)-crystallin, Heat shock protein beta-5 Details: Hexameric phosphorylation-mimicking mutant of human alphaB-crystallin Oligomeric state: Hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 121 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Alpha-crystallin B chain |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 / Details: PBS |
Staining | Type: NEGATIVE / Details: Cryo |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
-Electron microscopy
Microscope | OTHER |
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Date | Sep 2, 2010 |
Image recording | Digitization - Scanner: OTHER |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 49415 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: Each negative |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Number images used: 5617 |