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- EMDB-53389: Asgard HHoB open hypernucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-53389
TitleAsgard HHoB open hypernucleosome
Map dataHHoB Asgard open hypernucleosome
Sample
  • Complex: Asgard HHoB hypernucleosome in the open state
Keywordsarchaea / chromatin / histone / DNA / Asgard / nucleosome / DNA BINDING PROTEIN
Biological speciesCandidatus Heimdallarchaeota archaeon LC_3 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsRanawat HM / Dodonova SO
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)3DchromArchaea 101076671European Union
CitationJournal: Mol Cell / Year: 2025
Title: Cryo-EM reveals open and closed Asgard chromatin assemblies.
Authors: Harsh M Ranawat / Marc K Cajili / Natalia Lopez-Barbosa / Thomas Quail / Remus T Dame / Svetlana O Dodonova /
Abstract: Asgards are the closest archaeal relatives of eukaryotes, representing an important step in chromatin evolution. However, their chromatin organization has remained enigmatic until now. In this study, ...Asgards are the closest archaeal relatives of eukaryotes, representing an important step in chromatin evolution. However, their chromatin organization has remained enigmatic until now. In this study, we present the first structures of Asgard chromatin assemblies formed by the Hodarchaeal histone HHoB. Our high-resolution cryo-electron microscopy (cryo-EM) structures reveal that this Asgard histone assembles into compact "closed" and into extended "open" hypernucleosomes. Thus, the closed hypernucleosome conformation is conserved across archaeal lineages, while the open conformation resembles a eukaryotic H3-H4 octasome and likely represents an Asgard-specific innovation. Moreover, we show that Mg²⁺ ions influence Asgard chromatin conformation, suggesting a regulatory role. Overall, our study provides the first structure-based model of Asgard chromatin organization, expanding our understanding of chromatin architecture in an evolutionary context.
History
DepositionApr 11, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53389.png

Downloads & links

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Map

FileDownload / File: emd_53389.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHHoB Asgard open hypernucleosome
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 263.04 Å		0.82 Å/pix.
x 320 pix.
= 263.04 Å		0.82 Å/pix.
x 320 pix.
= 263.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.029772716 - 0.16030785
Average (Standard dev.)0.0013306553 (±0.009266555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53389_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: half map B

Fileemd_53389_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_53389_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Asgard HHoB hypernucleosome in the open state

EntireName: Asgard HHoB hypernucleosome in the open state
Components
  • Complex: Asgard HHoB hypernucleosome in the open state

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Supramolecule #1: Asgard HHoB hypernucleosome in the open state

SupramoleculeName: Asgard HHoB hypernucleosome in the open state / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon LC_3 (archaea)

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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
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
100.0 mMNaClNaCl
20.0 mMMgCl2MgCl2

Details: 20 mM HEPES pH 7.5, 100 mM NaCl, 20mM MgCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 63.84 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 214840
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio reconstruction in cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 40918
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Homogenous Refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Homogenous refinement
FSC plot (resolution estimation)

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