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Yorodumi- EMDB-12766: Single particle cryo-EM reconstruction of just the top two rings ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12766 | |||||||||
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Title | Single particle cryo-EM reconstruction of just the top two rings of a 40-mer assembly of recombinant yeast Hsp26 S207E mutant. | |||||||||
Map data | Cryo-EM Single particle Reconstruction of the top two rings of a 40mer oligomer of yeast Hsp26 S207E mutant, containing 16 monomers. This map was used for flexible fitting of the atomic model | |||||||||
Sample |
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Keywords | small heat shock proteins / Hsp26 S207E mutant / CHAPERONE | |||||||||
Function / homology | Function and homology information cytoplasmic stress granule / unfolded protein binding / protein folding / cellular response to heat / mRNA binding / mitochondrion / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.8 Å | |||||||||
Authors | Muehlhofer M / Peters C / Kriehuber T / Kreuzeder M / Kazman P / Rodina N / Reif B / Haslbeck M / Weinkauf S / Buchner J | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Phosphorylation activates the yeast small heat shock protein Hsp26 by weakening domain contacts in the oligomer ensemble. Authors: Moritz Mühlhofer / Carsten Peters / Thomas Kriehuber / Marina Kreuzeder / Pamina Kazman / Natalia Rodina / Bernd Reif / Martin Haslbeck / Sevil Weinkauf / Johannes Buchner / Abstract: Hsp26 is a small heat shock protein (sHsp) from S. cerevisiae. Its chaperone activity is activated by oligomer dissociation at heat shock temperatures. Hsp26 contains 9 phosphorylation sites in ...Hsp26 is a small heat shock protein (sHsp) from S. cerevisiae. Its chaperone activity is activated by oligomer dissociation at heat shock temperatures. Hsp26 contains 9 phosphorylation sites in different structural elements. Our analysis of phospho-mimetic mutations shows that phosphorylation activates Hsp26 at permissive temperatures. The cryo-EM structure of the Hsp26 40mer revealed contacts between the conserved core domain of Hsp26 and the so-called thermosensor domain in the N-terminal part of the protein, which are targeted by phosphorylation. Furthermore, several phosphorylation sites in the C-terminal extension, which link subunits within the oligomer, are sensitive to the introduction of negative charges. In all cases, the intrinsic inhibition of chaperone activity is relieved and the N-terminal domain becomes accessible for substrate protein binding. The weakening of domain interactions within and between subunits by phosphorylation to activate the chaperone activity in response to proteotoxic stresses independent of heat stress could be a general regulation principle of sHsps. | |||||||||
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_12766.map.gz | 85.7 MB | EMDB map data format | |
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Header (meta data) | emd-12766-v30.xml emd-12766.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12766_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_12766.png | 174.4 KB | ||
Filedesc metadata | emd-12766.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12766 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12766 | HTTPS FTP |
-Validation report
Summary document | emd_12766_validation.pdf.gz | 567.2 KB | Display | EMDB validaton report |
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Full document | emd_12766_full_validation.pdf.gz | 566.8 KB | Display | |
Data in XML | emd_12766_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | emd_12766_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12766 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12766 | HTTPS FTP |
-Related structure data
Related structure data | 7oa6MC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12766.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM Single particle Reconstruction of the top two rings of a 40mer oligomer of yeast Hsp26 S207E mutant, containing 16 monomers. This map was used for flexible fitting of the atomic model | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.33 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 : Top two rings (16 subunits) of a 40mer complex of Hsp26 mutant S2...
Entire | Name: Top two rings (16 subunits) of a 40mer complex of Hsp26 mutant S207E. (use 0.487 as threshold to visualise) |
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Components |
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-Supramolecule #1: Top two rings (16 subunits) of a 40mer complex of Hsp26 mutant S2...
Supramolecule | Name: Top two rings (16 subunits) of a 40mer complex of Hsp26 mutant S207E. (use 0.487 as threshold to visualise) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 382 KDa |
-Macromolecule #1: Heat shock protein 26
Macromolecule | Name: Heat shock protein 26 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 23.910586 KDa |
Recombinant expression | Organism: Escherichia coli HB101 (bacteria) |
Sequence | String: MSFNSPFFDF FDNINNEVDA FNRLLGEGGL RGYAPRRQLA NTPAKDSTGK EVARPNNYAG ALYDPRDETL DDWFDNDLSL FPSGFGFPR SVAVPVDILD HDNNYELKVV VPGVKSKKDI DIEYHQNKNQ ILVSGEIPST LNEESKDKVK VKESSSGKFK R VITLPDYP ...String: MSFNSPFFDF FDNINNEVDA FNRLLGEGGL RGYAPRRQLA NTPAKDSTGK EVARPNNYAG ALYDPRDETL DDWFDNDLSL FPSGFGFPR SVAVPVDILD HDNNYELKVV VPGVKSKKDI DIEYHQNKNQ ILVSGEIPST LNEESKDKVK VKESSSGKFK R VITLPDYP GVDADNIKAD YANGVLTLTV PKLKPQKDGK NHVKKIEVSS QESWGN UniProtKB: Heat shock protein 26 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 5010 / Average exposure time: 8.0 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | Homology model generated with ITASSER with 1GME as template. Fitted with Chimera and flexibly fitted with NAMD. Residues 63 to 214 present in the model. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient |
Output model | PDB-7oa6: |