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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: Ranawat, H.M. / Cajili, M.K. / Lopez-Barbosa, N. / Quail, T. / Dame, R.T. / Dodonova, S.O.
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

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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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