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- EMDB-35069: Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis -

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Basic information

Entry
Database: EMDB / ID: EMD-35069
TitleCryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis
Map data
Sample
  • Complex: Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis
    • Protein or peptide: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
KeywordsCryo-EM / N15MsDps2 / DNA BINDING PROTEIN
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding / DNA binding
Similarity search - Function
Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Starvation-inducible DNA-binding protein or fine tangled pili major subunit
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsGarg P / Dutta S
Funding support India, 2 items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India) India
Department of Biotechnology (DBT, India) India
CitationJournal: 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
DepositionJan 3, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35069.png

Downloads & links

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Map

FileDownload / File: emd_35069.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 240 pix.
= 220.8 Å		0.92 Å/pix.
x 240 pix.
= 220.8 Å		0.92 Å/pix.
x 240 pix.
= 220.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.408
Minimum - Maximum-0.84439665 - 1.4379842
Average (Standard dev.)0.0026558237 (±0.076936364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 220.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35069_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_35069_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis

EntireName: Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis
Components
  • Complex: Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis
    • Protein or peptide: Starvation-inducible DNA-binding protein or fine tangled pili major subunit

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Supramolecule #1: Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis

SupramoleculeName: Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: Starvation-inducible DNA-binding protein or fine tangled pili maj...

MacromoleculeName: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 16.163995 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
TPEFGGNLQK VLVDLIELSL QGKQAHWNVV GSNFRDLHLQ LDELVDFARE GSDTIAERMR ALDAVPDGRS DTVAATTTLP EFPAFERST ADVVDLITTR INATVDTIRR VHDAVDAEDP STADLLHGLI DGLEKQAWLI RSENRKV

UniProtKB: Starvation-inducible DNA-binding protein or fine tangled pili major subunit

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2z90

Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27741
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8hwz:
Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis

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