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- EMDB-53387: Asgard HHoB hypernucleosome in the closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-53387
TitleAsgard HHoB hypernucleosome in the closed state
Map dataAsgard HHoB closed hypernucleosome
Sample
  • Complex: Closed hypernucleosome assembled from HHoB Asgard archaeal histone and DNA
    • Protein or peptide: Archaeal histone A
    • DNA: DNA (180-MER)
    • DNA: DNA (180-MER)
Keywordsarchaea / Asgard / chromatin / histone / DNA / nucleosome / DNA BINDING PROTEIN
Function / homology:
Function and homology information
Biological speciesCandidatus Heimdallarchaeota archaeon LC_3 (archaea) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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_53387.png

Downloads & links

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Map

FileDownload / File: emd_53387.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsgard HHoB closed hypernucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 320 pix.
= 206.4 Å		0.65 Å/pix.
x 320 pix.
= 206.4 Å		0.65 Å/pix.
x 320 pix.
= 206.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.645 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.1007107 - 0.18980798
Average (Standard dev.)0.00034332502 (±0.008180651)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 206.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53387_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_53387_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_53387_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Closed hypernucleosome assembled from HHoB Asgard archaeal histon...

EntireName: Closed hypernucleosome assembled from HHoB Asgard archaeal histone and DNA
Components
  • Complex: Closed hypernucleosome assembled from HHoB Asgard archaeal histone and DNA
    • Protein or peptide: Archaeal histone A
    • DNA: DNA (180-MER)
    • DNA: DNA (180-MER)

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Supramolecule #1: Closed hypernucleosome assembled from HHoB Asgard archaeal histon...

SupramoleculeName: Closed hypernucleosome assembled from HHoB Asgard archaeal histone and DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: in presence of 100 mM Mg
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon LC_3 (archaea)
Molecular weightTheoretical: 164 KDa

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Macromolecule #1: Archaeal histone A

MacromoleculeName: Archaeal histone A / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon LC_3 (archaea)
Molecular weightTheoretical: 7.796902 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SNAMAGNFAN ARVEKLIRQA GAQRVSADAV DKMNEILTDW GKNIAKYAVE IARHSGRKTV KENDIKLAAQ K

UniProtKB: UNIPROTKB: A0A1Q9NRY6

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Macromolecule #2: DNA (180-MER)

MacromoleculeName: DNA (180-MER) / type: dna / ID: 2
Details: 147 bp Widom 601 - in a continuous super helix (Widom601-Widom601-etc)
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 55.36323 KDa
SequenceString: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String:
(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT)(DC)(DT)(DG)(DG)(DA)(DG) (DA)(DA)(DT)(DC)(DC)(DC)(DG) (DG)(DT) (DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG) (DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)

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Macromolecule #3: DNA (180-MER)

MacromoleculeName: DNA (180-MER) / type: dna / ID: 3
Details: 147 bp Widom 601 - in a continuous super helix (Widom601-Widom601-etc)
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 55.781512 KDa
SequenceString: (DC)(DA)(DA)(DT)(DT)(DG)(DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DA)(DC)(DA)(DG)(DG)(DA) (DT) (DG)(DT)(DA)(DT)(DA)(DT) ...String:
(DC)(DA)(DA)(DT)(DT)(DG)(DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DA)(DC)(DA)(DG)(DG)(DA) (DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG) (DC)(DC) (DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA) (DT)(DC)(DC) (DC)(DC)(DT)(DT)(DG)(DG) (DC)(DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC) (DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC) (DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC)(DG) (DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA) (DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG)(DT) (DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC) (DT)(DC) (DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA) (DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG)

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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

Concentration0.465 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
100.0 mMNaClSodium Chloride
100.0 mMMgCl2Magnesium Chloride

Details: 20 mM HEPES pH 7.5, 100 mM NaCl, 100 mM MgCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 200 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: at 20* C.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 39.93 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: 1.5 µm / Nominal defocus min: 0.5 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: 4964843
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Cylinder of outer diameter 13nm and inner diameter 1nm.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 353468
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.4.1)
Software - details: Helical refinement with cylindrical initial model
Details: in-plane rotations from filament tracer
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Software - details: Helical refinement with non-uniform refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

nry6

chain_id: A, residue_range: 1-68, source_name: AlphaFold, initial_model_type: in silico modelMonomer prediction of HHoB

5t5k

chain_id: I, residue_range: 1-90, source_name: PDB, initial_model_type: experimental modelDNA monomer

5t5k

chain_id: J, residue_range: 1-90, source_name: PDB, initial_model_type: experimental modelDNA monomer
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9qv6:
Asgard HHoB hypernucleosome in the closed state

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