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Yorodumi- EMDB-35071: Focused cryo-EM map of MsDps2 from MsDps2-DNA complex of Mycobact... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35071 | |||||||||
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Title | Focused cryo-EM map of MsDps2 from MsDps2-DNA complex of Mycobacterium smegmatis | |||||||||
Map data | ||||||||||
Sample |
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Keywords | MsDps2 / cryo-EM / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on metal ions / ferric iron binding / DNA binding Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.29 Å | |||||||||
Authors | Dutta S / Garg P | |||||||||
Funding support | India, 2 items
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Citation | Journal: J Mol Biol / Year: 2024 Title: Cryo-EM Reveals the Mechanism of DNA Compaction by Mycobacterium smegmatis Dps2. Authors: Priyanka Garg / Thejas Satheesh / Mahipal Ganji / Somnath Dutta / Abstract: DNA binding protein from starved cells (Dps) is a miniature ferritin complex, which plays a vital role in protecting bacterial DNA during starvation to maintain the integrity of bacteria under ...DNA binding protein from starved cells (Dps) is a miniature ferritin complex, which plays a vital role in protecting bacterial DNA during starvation to maintain the integrity of bacteria under hostile conditions. Several approaches, including cryo-electron tomography, have been previously implemented by other research groups to decipher the structure of the Dps protein bound to DNA. However, none of the structures of the Dps-DNA complex was resolved to high resolution to identify the DNA binding residues. Like other bacteria, Mycobacterium smegmatis also expresses Dps2 (called MsDps2), which binds DNA to protect it under oxidative stress conditions. In this study, we implemented various biochemical and biophysical studies to characterize the DNA protein interactions of Dps2 protein from Mycobacterium smegmatis. We employed single-particle cryo-EM-based structural analysis of MsDps2-DNA complexes and identified that the region close to the N-terminus confers the DNA binding property. Based on cryo-EM data, we also pinpointed several arginine residues, proximal to the DNA binding region, responsible for DNA binding. We also performed mutations of these residues, which dramatically reduced the MsDps2-DNA interaction. In addition, we proposed a model that elucidates the mechanism of DNA compaction, which adapts a lattice-like structure. We performed single-molecule imaging of MsDps2-DNA interactions that corroborate well with our structural studies. Taken together, our results delineate the specific MsDps2 residues that play an important role in DNA binding and compaction, providing new insights into Mycobacterial DNA compaction mechanisms under stress conditions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35071.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-35071-v30.xml emd-35071.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35071_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_35071.png | 141 KB | ||
Filedesc metadata | emd-35071.cif.gz | 4.9 KB | ||
Others | emd_35071_half_map_1.map.gz emd_35071_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35071 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35071 | HTTPS FTP |
-Validation report
Summary document | emd_35071_validation.pdf.gz | 862.9 KB | Display | EMDB validaton report |
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Full document | emd_35071_full_validation.pdf.gz | 862.5 KB | Display | |
Data in XML | emd_35071_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | emd_35071_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35071 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35071 | HTTPS FTP |
-Related structure data
Related structure data | 8hx1MC 8hwzC 8hx0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35071.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35071_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35071_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Focused cryo-EM map of MsDps2 from MsDps2-DNA complex of Mycobact...
Entire | Name: Focused cryo-EM map of MsDps2 from MsDps2-DNA complex of Mycobacterium smegmatis |
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Components |
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-Supramolecule #1: Focused cryo-EM map of MsDps2 from MsDps2-DNA complex of Mycobact...
Supramolecule | Name: Focused cryo-EM map of MsDps2 from MsDps2-DNA complex of Mycobacterium smegmatis type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
-Macromolecule #1: Putative starvation-induced DNA protecting protein/Ferritin and Dps
Macromolecule | Name: Putative starvation-induced DNA protecting protein/Ferritin and Dps type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Molecular weight | Theoretical: 17.854863 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSARRTESDI QGFHATPEFG GNLQKVLVDL IELSLQGKQA HWNVVGSNFR DLHLQLDELV DFAREGSDTI AERMRALDAV PDGRSDTVA ATTTLPEFPA FERSTADVVD LITTRINATV DTIRRVHDAV DAEDPSTADL LHGLIDGLEK QAWLIRSENR K V UniProtKB: Starvation-inducible DNA-binding protein or fine tangled pili major subunit |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |