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Yorodumi- EMDB-37712: Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37712 | ||||||||||||
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Title | Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5 | ||||||||||||
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Sample |
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Keywords | Hsp16.5 / molecular chaperone / oligomeric protein / small heat-shock protein / stress response / CHAPERONE | ||||||||||||
Biological species | Methanocaldococcus jannaschii DSM 2661 (archaea) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.02 Å | ||||||||||||
Authors | Lee J / Ryu B / Kim T / Kim KK | ||||||||||||
Funding support | Korea, Republic Of, 3 items
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Citation | Journal: Int J Biol Macromol / Year: 2024 Title: Cryo-EM structure of a 16.5-kDa small heat-shock protein from Methanocaldococcus jannaschii. Authors: Joohyun Lee / Bumhan Ryu / Truc Kim / Kyeong Kyu Kim / Abstract: The small heat-shock protein (sHSP) from the archaea Methanocaldococcus jannaschii, MjsHSP16.5, functions as a broad substrate ATP-independent holding chaperone protecting misfolded proteins from ...The small heat-shock protein (sHSP) from the archaea Methanocaldococcus jannaschii, MjsHSP16.5, functions as a broad substrate ATP-independent holding chaperone protecting misfolded proteins from aggregation under stress conditions. This protein is the first sHSP characterized by X-ray crystallography, thereby contributing significantly to our understanding of sHSPs. However, despite numerous studies assessing its functions and structures, the precise arrangement of the N-terminal domains (NTDs) within this sHSP cage remains elusive. Here we present the cryo-electron microscopy (cryo-EM) structure of MjsHSP16.5 at 2.49-Å resolution. The subunits of MjsHSP16.5 in the cryo-EM structure exhibit lesser compaction compared to their counterparts in the crystal structure. This structural feature holds particular significance in relation to the biophysical properties of MjsHSP16.5, suggesting a close resemblance to this sHSP native state. Additionally, our cryo-EM structure unveils the density of residues 24-33 within the NTD of MjsHSP16.5, a feature that typically remains invisible in the majority of its crystal structures. Notably, these residues show a propensity to adopt a β-strand conformation and engage in antiparallel interactions with strand β1, both intra- and inter-subunit modes. These structural insights are corroborated by structural predictions, disulfide bond cross-linking studies of Cys-substitution mutants, and protein disaggregation assays. A comprehensive understanding of the structural features of MjsHSP16.5 expectedly holds the potential to inspire a wide range of interdisciplinary applications, owing to the renowned versatility of this sHSP as a nanoscale protein platform. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37712.map.gz | 107.8 MB | EMDB map data format | |
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Header (meta data) | emd-37712-v30.xml emd-37712.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37712_fsc.xml | 14.4 KB | Display | FSC data file |
Images | emd_37712.png | 161.2 KB | ||
Masks | emd_37712_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-37712.cif.gz | 4.1 KB | ||
Others | emd_37712_additional_1.map.gz emd_37712_half_map_1.map.gz emd_37712_half_map_2.map.gz | 171.1 MB 170.7 MB 170.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37712 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37712 | HTTPS FTP |
-Validation report
Summary document | emd_37712_validation.pdf.gz | 980.8 KB | Display | EMDB validaton report |
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Full document | emd_37712_full_validation.pdf.gz | 980.4 KB | Display | |
Data in XML | emd_37712_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | emd_37712_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37712 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37712 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_37712.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.673 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_37712_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_37712_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_37712_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_37712_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5
Entire | Name: Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5 |
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Components |
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-Supramolecule #1: Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5
Supramolecule | Name: Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Methanocaldococcus jannaschii DSM 2661 (archaea) |
Molecular weight | Theoretical: 396 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.7 mg/mL |
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Buffer | pH: 7.2 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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