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- EMDB-52187: Amyloid DNA Bridging by Hfq C-terminal region -

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Basic information

Entry
Database: EMDB / ID: EMD-52187
TitleAmyloid DNA Bridging by Hfq C-terminal region
Map data
Sample
  • Complex: Hfq C-terminal amyloid domain bound to dsDNA(dA:dT)59
    • Protein or peptide: Hfq C-terminal
    • DNA: DNA (dA:dT)59
KeywordsAmyloid / Nucleoid Associated Protein NAP / DNA bridging / DNA BINDING PROTEIN
Function / homology
Function and homology information


sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / bacterial nucleoid / regulation of translation, ncRNA-mediated / bent DNA binding / regulation of RNA stability / RNA folding chaperone / tRNA processing / tRNA binding / regulation of DNA-templated transcription ...sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / bacterial nucleoid / regulation of translation, ncRNA-mediated / bent DNA binding / regulation of RNA stability / RNA folding chaperone / tRNA processing / tRNA binding / regulation of DNA-templated transcription / DNA binding / RNA binding / ATP binding / cytosol
Similarity search - Function
RNA-binding protein Hfq / Hfq protein / : / Sm domain profile. / LSM domain superfamily
Similarity search - Domain/homology
RNA-binding protein Hfq
Similarity search - Component
Biological speciesE. coli K12 (bacteria) / Escherichia coli (E. coli) / synthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 19.0 Å
AuthorsGragera M / Arluison V
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Amyloid-like DNA bridging: a new mode of DNA shaping.
Authors: Frank Wien / Marcos Gragera / Tatsuhito Matsuo / Gautier Moroy / María Teresa Bueno-Carrasco / Rocío Arranz / Antoine Cossa / Anne Martel / Heloisa N Bordallo / Svemir Rudić / Marisela ...Authors: Frank Wien / Marcos Gragera / Tatsuhito Matsuo / Gautier Moroy / María Teresa Bueno-Carrasco / Rocío Arranz / Antoine Cossa / Anne Martel / Heloisa N Bordallo / Svemir Rudić / Marisela Velez / Johan R C van der Maarel / Judith Peters / Véronique Arluison /
Abstract: All organisms depend on specific proteins to compact and organize their genomes. In eukaryotes, histones fulfil this role, while bacterial chromosomes are shaped by nucleoid-associated proteins (NAPs) ...All organisms depend on specific proteins to compact and organize their genomes. In eukaryotes, histones fulfil this role, while bacterial chromosomes are shaped by nucleoid-associated proteins (NAPs). Among its pleiotropic functions, the NAP Hfq plays a pivotal role in bacterial genome organization. In this study, we characterized the structure of the C-terminal extension of Hfq, which mediates chromosomal compaction, in its DNA-bound state. Using an integrative approach that combined transmission electron microscopy, neutron scattering, site-directed mutagenesis, and molecular modeling, we identified an amyloid module formed by the C-terminal region of Hfq. This module uniquely bridges and compacts six DNA molecules, marking the first documented instance of an amyloid structure with DNA-bridging properties. Our findings redefine the functional landscape of amyloids, linking them to genome architecture and gene regulation. This result suggests that amyloid-DNA interactions may represent a conserved mechanism across biological systems, with profound implications for understanding genome organization and the regulation of gene expression in both prokaryotes and eukaryotes.
History
DepositionNov 25, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52187.png

Downloads & links

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Map

FileDownload / File: emd_52187.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 580 pix.
= 794.6 Å		1.37 Å/pix.
x 580 pix.
= 794.6 Å		1.37 Å/pix.
x 580 pix.
= 794.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-0.5906752 - 2.3492851
Average (Standard dev.)-0.00046699183 (±0.10818693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions580580580
Spacing580580580
CellA=B=C: 794.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52187_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52187_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Hfq C-terminal amyloid domain bound to dsDNA(dA:dT)59

EntireName: Hfq C-terminal amyloid domain bound to dsDNA(dA:dT)59
Components
  • Complex: Hfq C-terminal amyloid domain bound to dsDNA(dA:dT)59
    • Protein or peptide: Hfq C-terminal
    • DNA: DNA (dA:dT)59

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Supramolecule #1: Hfq C-terminal amyloid domain bound to dsDNA(dA:dT)59

SupramoleculeName: Hfq C-terminal amyloid domain bound to dsDNA(dA:dT)59 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Hfq C-terminal region, 38 aa, SRPVSHHSNNAGGGTSSNYHHGSSAQNTSAQQDSEETE DNA (dA:dT)59 Chemical synthesis
Source (natural)Organism: E. coli K12 (bacteria)

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Macromolecule #1: Hfq C-terminal

MacromoleculeName: Hfq C-terminal / type: protein_or_peptide / ID: 1 / Details: DNA:protein complex / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655
SequenceString:
SRPVSHHSNN AGGGTSSNYH HGSSAQNTSA QQDSEETE

UniProtKB: RNA-binding protein Hfq

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Macromolecule #2: DNA (dA:dT)59

MacromoleculeName: DNA (dA:dT)59 / type: dna / ID: 2
Details: Double stranded (ds) DNA sequence: (dA:dT)59. The choice of this 59-basepair homo-polymeric DNA sequence was made because Hfq has highest affinity for A-rich sequences.
Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 5 / Details: water
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample consisted in the amyloid structure formed by Hfq CTR region (38 amino acid residues) bound to a double stranded (ds) DNA sequence: (dA:dT)59 prepared in water at 20 mg/mL and then diluted. The molar ratio DNA:CTR was 4:1 (DNA concentration expressed in base-pair). Samples were analyzed after 4 weeks to allow complex full self-assembly.

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.2 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 1.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 0 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 27059
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 59043
Startup modelType of model: NONE / Details: cryoSPARC ab initio
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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