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Yorodumi- EMDB-29913: Cryo-EM 3D map of the Mycobacterium tuberculosis Hsp70 protein Dn... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29913 | |||||||||
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Title | Cryo-EM 3D map of the Mycobacterium tuberculosis Hsp70 protein DnaK bound to the nucleotide exchange factor GrpE | |||||||||
Map data | processed by DeepEMhancer | |||||||||
Sample |
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Keywords | heat shock protein 70 / nucleotide exchange factor / protein folding and refolding / CHAPERONE | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Xiao X / Li H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structure of the M. tuberculosis DnaK-GrpE complex reveals how key DnaK roles are controlled. Authors: Xiansha Xiao / Allison Fay / Pablo Santos Molina / Amanda Kovach / Michael S Glickman / Huilin Li / Abstract: The molecular chaperone DnaK is essential for viability of Mycobacterium tuberculosis (Mtb). DnaK hydrolyzes ATP to fold substrates, and the resulting ADP is exchanged for ATP by the nucleotide ...The molecular chaperone DnaK is essential for viability of Mycobacterium tuberculosis (Mtb). DnaK hydrolyzes ATP to fold substrates, and the resulting ADP is exchanged for ATP by the nucleotide exchange factor GrpE. It has been unclear how GrpE couples DnaK's nucleotide exchange with substrate release. Here we report a cryo-EM analysis of GrpE bound to an intact Mtb DnaK, revealing an asymmetric 1:2 DnaK-GrpE complex. The GrpE dimer ratchets to modulate both DnaK nucleotide-binding domain and the substrate-binding domain. We further show that the disordered GrpE N-terminus is critical for substrate release, and that the DnaK-GrpE interface is essential for protein folding activity both in vitro and in vivo. Therefore, the Mtb GrpE dimer allosterically regulates DnaK to concomitantly release ADP in the nucleotide-binding domain and substrate peptide in the substrate-binding domain. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29913.map.gz | 109.7 MB | EMDB map data format | |
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Header (meta data) | emd-29913-v30.xml emd-29913.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
Images | emd_29913.png | 66.6 KB | ||
Filedesc metadata | emd-29913.cif.gz | 4.5 KB | ||
Others | emd_29913_half_map_1.map.gz emd_29913_half_map_2.map.gz | 116.2 MB 116.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29913 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29913 | HTTPS FTP |
-Validation report
Summary document | emd_29913_validation.pdf.gz | 698.3 KB | Display | EMDB validaton report |
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Full document | emd_29913_full_validation.pdf.gz | 697.9 KB | Display | |
Data in XML | emd_29913_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_29913_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29913 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29913 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29913.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | processed by DeepEMhancer | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_29913_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29913_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Binary complex of DnaK with nucleotide exchange factor GrpE
Entire | Name: Binary complex of DnaK with nucleotide exchange factor GrpE |
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Components |
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-Supramolecule #1: Binary complex of DnaK with nucleotide exchange factor GrpE
Supramolecule | Name: Binary complex of DnaK with nucleotide exchange factor GrpE type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R2/1 / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 15720 / Average exposure time: 1.5 sec. / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 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 |