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- EMDB-53390: Asgard HHoB nucleosome map in the open state in 0mM MgCl2 -

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Basic information

Entry
Database: EMDB / ID: EMD-53390
TitleAsgard HHoB nucleosome map in the open state in 0mM MgCl2
Map data
Sample
  • Complex: Open complex of HHoB Asgard archaeal histone and DNA
Keywordsarchaea / chromatin / histone / DNA / Asgard / nucleosome / DNA BINDING PROTEIN
Biological speciesCandidatus Heimdallarchaeota archaeon LC_3 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.44 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_53390.png

Downloads & links

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Map

FileDownload / File: emd_53390.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.10901597 - 0.44479045
Average (Standard dev.)0.0010303534 (±0.016919782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53390_msk_1.map
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Half map: #1

Fileemd_53390_half_map_1.map
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Half map: #2

Fileemd_53390_half_map_2.map
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Sample components

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Entire : Open complex of HHoB Asgard archaeal histone and DNA

EntireName: Open complex of HHoB Asgard archaeal histone and DNA
Components
  • Complex: Open complex of HHoB Asgard archaeal histone and DNA

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Supramolecule #1: Open complex of HHoB Asgard archaeal histone and DNA

SupramoleculeName: Open complex of HHoB Asgard archaeal histone and DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Open state of the HHoB nucleosome, reconstituted in vitro
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon LC_3 (archaea)
Molecular weightTheoretical: 137 KDa

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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

Concentration0.192 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
100.0 mMNaClsodium chloride

Details: 20 mM HEPES pH 7.5, 100 mM NaCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / 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 / Details: at 20* C.
Details20 mM HEPES pH 7.5, 100 mM NaCl

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 46.63 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: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
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: 3108514
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 96361
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Non-uniform refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Non-uniform refinement
FSC plot (resolution estimation)

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