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- EMDB-3459: Hsp21 dodecamer, structural model based on cryo-EM and homology m... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3459 | |||||||||
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Title | Hsp21 dodecamer, structural model based on cryo-EM and homology modelling | |||||||||
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Function / homology | ![]() chloroplast nucleoid / chloroplast organization / protein folding chaperone complex / response to light stimulus / response to heat / regulation of DNA-templated transcription Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
![]() | Rutsdottir G / Harmark J / Koeck PJB / Hebert H / Soderberg CAG / Emanuelsson C | |||||||||
![]() | ![]() Title: Structural model of dodecameric heat-shock protein Hsp21: Flexible N-terminal arms interact with client proteins while C-terminal tails maintain the dodecamer and chaperone activity. Authors: Gudrun Rutsdottir / Johan Härmark / Yoran Weide / Hans Hebert / Morten I Rasmussen / Sven Wernersson / Michal Respondek / Mikael Akke / Peter Højrup / Philip J B Koeck / Christopher A G ...Authors: Gudrun Rutsdottir / Johan Härmark / Yoran Weide / Hans Hebert / Morten I Rasmussen / Sven Wernersson / Michal Respondek / Mikael Akke / Peter Højrup / Philip J B Koeck / Christopher A G Söderberg / Cecilia Emanuelsson / ![]() ![]() Abstract: Small heat-shock proteins (sHsps) prevent aggregation of thermosensitive client proteins in a first line of defense against cellular stress. The mechanisms by which they perform this function have ...Small heat-shock proteins (sHsps) prevent aggregation of thermosensitive client proteins in a first line of defense against cellular stress. The mechanisms by which they perform this function have been hard to define due to limited structural information; currently, there is only one high-resolution structure of a plant sHsp published, that of the cytosolic Hsp16.9. We took interest in Hsp21, a chloroplast-localized sHsp crucial for plant stress resistance, which has even longer N-terminal arms than Hsp16.9, with a functionally important and conserved methionine-rich motif. To provide a framework for investigating structure-function relationships of Hsp21 and understanding these sequence variations, we developed a structural model of Hsp21 based on homology modeling, cryo-EM, cross-linking mass spectrometry, NMR, and small-angle X-ray scattering. Our data suggest a dodecameric arrangement of two trimer-of-dimer discs stabilized by the C-terminal tails, possibly through tail-to-tail interactions between the discs, mediated through extended IVI motifs. Our model further suggests that six N-terminal arms are located on the outside of the dodecamer, accessible for interaction with client proteins, and distinct from previous undefined or inwardly facing arms. To test the importance of the IVI motif, we created the point mutant V181A, which, as expected, disrupts the Hsp21 dodecamer and decreases chaperone activity. Finally, our data emphasize that sHsp chaperone efficiency depends on oligomerization and that client interactions can occur both with and without oligomer dissociation. These results provide a generalizable workflow to explore sHsps, expand our understanding of sHsp structural motifs, and provide a testable Hsp21 structure model to inform future investigations. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11 KB 11 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.4 KB | Display | ![]() |
Images | ![]() | 59.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nmsMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Hsp21 dodecamer
Entire | Name: Hsp21 dodecamer |
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Components |
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-Supramolecule #1: Hsp21 dodecamer
Supramolecule | Name: Hsp21 dodecamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Experimental: 252 KDa |
-Macromolecule #1: 25.3 kDa heat shock protein, chloroplastic
Macromolecule | Name: 25.3 kDa heat shock protein, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 16.393787 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: LLDPLSPMRT MRQMLDTMDR MFEDTMPVSG RNRGGSGVSE IRAPWDIKEE EHEIKMRFDM PGLSKEDVKI SVEDNVLVIK GEQKKEDSD DSWSGRSVSS YGTRLQLPDN CEKDKIKAEL KNGVLFITIP KTKVERKVID VQIQ |
-Macromolecule #2: 25.3 kDa heat shock protein, chloroplastic
Macromolecule | Name: 25.3 kDa heat shock protein, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.777428 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: RAPWDIKEEE HEIKMRFDMP GLSKEDVKIS VEDNVLVIKG EQKKEDSDDS WSGRSVSSYG TRLQLPDNCE KDKIKAELKN GVLFITIPK TKVERKVIDV QIQ |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R2/4 / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | JEOL 2100F |
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Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 1.4 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |