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- EMDB-53388: Asgard HHoB nucleosome in the open state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53388
TitleAsgard HHoB nucleosome in the open state
Map dataHHoB nucleosome in the open conformation
Sample
  • Complex: Open complex of HHoB Asgard archaeal histone and DNA
    • Protein or peptide: Archaeal histone A
    • DNA: DNA (120-MER) from Widom601
    • DNA: DNA (120-MER) from Widom601
Keywordsarchaea / chromatin / histone / DNA / Asgard / 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: 3.6 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_53388.png

Downloads & links

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Map

FileDownload / File: emd_53388.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHHoB nucleosome in the open conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.37 Å/pix.
x 576 pix.
= 210.24 Å		0.37 Å/pix.
x 576 pix.
= 210.24 Å		0.37 Å/pix.
x 576 pix.
= 210.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.365 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.053097084 - 0.085465215
Average (Standard dev.)-0.0010305974 (±0.0024526375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 210.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53388_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_53388_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_53388_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 : 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
    • Protein or peptide: Archaeal histone A
    • DNA: DNA (120-MER) from Widom601
    • DNA: DNA (120-MER) from Widom601

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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: all
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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Macromolecule #1: Archaeal histone A

MacromoleculeName: Archaeal histone A / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon LC_3 (archaea)
Strain: LC_3
Molecular weightTheoretical: 7.524643 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGNFANARV EKLIRQAGAQ RVSADAVDKM NEILTDWGKN IAKYAVEIAR HSGRKTVKEN DIKLAAQK

UniProtKB: UNIPROTKB: A0A1Q9NRY6

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Macromolecule #2: DNA (120-MER) from Widom601

MacromoleculeName: DNA (120-MER) from Widom601 / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 36.849469 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #3: DNA (120-MER) from Widom601

MacromoleculeName: DNA (120-MER) from Widom601 / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 37.218699 KDa
SequenceString: (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) ...String:
(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)

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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
1.0 mMMgCl2Magnesium chloride

Details: 20 mM HEPES pH 7.5, 100 mM NaCl, 1mM MgCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 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, 1mM MgCl2

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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: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Average electron dose: 59.44 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: 165000
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 correctionType: 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Details: in cryosparc / Number images used: 96738
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Ab-initio reconstruction
Details: stochastic gradient descent (SGD), which optimizes particle poses by iteratively minimizing the alignment error. In cryoSparc
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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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 predication of HHoB

7x58

chain_id: I, residue_range: 1-120, source_name: PDB, initial_model_type: experimental modelDNA monomer

7x58

chain_id: J, residue_range: -59-0, source_name: PDB, initial_model_type: experimental modelDNA monomer
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qv7:
Asgard HHoB nucleosome in the open state

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