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

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Basic information

Entry
Database: PDB / ID: 9qv6
TitleAsgard HHoB hypernucleosome in the closed state
Components
  • (DNA (180-MER)) x 2
  • Archaeal histone A
KeywordsDNA BINDING PROTEIN / archaea / Asgard / chromatin / histone / DNA / nucleosome
Function / homologyDNA / DNA (> 10) / DNA (> 100) / :
Function and homology information
Biological speciesCandidatus Heimdallarchaeota archaeon LC_3 (archaea)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsRanawat, H.M. / Dodonova, S.O.
Funding supportEuropean Union, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Nov 12, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.3Dec 3, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Archaeal histone A
B: Archaeal histone A
C: Archaeal histone A
D: Archaeal histone A
E: Archaeal histone A
F: Archaeal histone A
G: Archaeal histone A
H: Archaeal histone A
I: Archaeal histone A
J: Archaeal histone A
K: Archaeal histone A
L: Archaeal histone A
X: DNA (180-MER)
Y: DNA (180-MER)


Theoretical massNumber of molelcules
Total (without water)204,70814
Polymers204,70814
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Archaeal histone A


Mass: 7796.902 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: GCA_001940645.1
Source: (gene. exp.) Candidatus Heimdallarchaeota archaeon LC_3 (archaea)
Gene: HeimC3_17480 / Details (production host): MacroLabs LIC-1B / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9NRY6
#2: DNA chain DNA (180-MER)


Mass: 55363.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PCR / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (180-MER)


Mass: 55781.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PCR / Source: (synth.) synthetic construct (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Closed hypernucleosome assembled from HHoB Asgard archaeal histone and DNA
Type: COMPLEX / Details: in presence of 100 mM Mg / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.164 MDa / Experimental value: NO
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon LC_3 (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 20 mM HEPES pH 7.5, 100 mM NaCl, 100 mM MgCl2
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESHEPES1
2100 mMSodium ChlorideNaCl1
3100 mMMagnesium ChlorideMgCl21
SpecimenConc.: 0.465 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: at 20* C

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 39.93 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4.1particle selectionusing filament picker
2SerialEMimage acquisition
7UCSF ChimeraX4.4.1model fittingRigid body fit
9cryoSPARC4.4.1initial Euler assignmentHelical refinement with cylindrical initial model
10cryoSPARC4.4.1final Euler assignmentHelical refinement with non-uniform refinement
12cryoSPARC4.4.13D reconstruction
13PHENIX1.21.1model refinementReal space refinement
14Coot0.9.8.93model refinementResidue fitting with helical and DNA-B form restraints
15UCSF ChimeraX1.7,1model refinementRelaxation into density using ISOLDE
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4964843
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 353468 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDChain residue rangeDetailsInitial refinement model-IDSource nameTypePdb chain residue range
1A0A1Q9NRY6A1-68Monomer prediction of HHoB1AlphaFoldin silico model
25T5K

5t5k

I5T5KI1-90DNA monomer2PDBexperimental model1-90
35T5K

5t5k

J5T5KJ1-90DNA monomer2PDBexperimental model1-90

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