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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: Ranawat HM / Cajili MK / Lopez-Barbosa N / Quail T / Dame RT / Dodonova SO
History
DepositionApr 11, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 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

Projections

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)
Density Histograms

Histogram

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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