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- PDB-9qv5: Asgard Archaeal HHoB nucleosome in the closed conformation -

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Basic information

Entry
Database: PDB / ID: 9qv5
TitleAsgard Archaeal HHoB nucleosome in the closed conformation
Components
  • (DNA (120-MER) part of a full 147 bp Widom601 DNA) x 2
  • Archaeal histone A
KeywordsDNA BINDING PROTEIN / Archaea / Asgard / chromatin / 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: 3.5 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
X: DNA (120-MER) part of a full 147 bp Widom601 DNA
Y: DNA (120-MER) part of a full 147 bp Widom601 DNA


Theoretical massNumber of molelcules
Total (without water)134,26510
Polymers134,26510
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: 7524.643 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: GCA_001940645.1
Source: (gene. exp.) Candidatus Heimdallarchaeota archaeon LC_3 (archaea)
Strain: LC_3 / Gene: HeimC3_17480 / Plasmid: MacroLabs LIC-1B / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9NRY6
#2: DNA chain DNA (120-MER) part of a full 147 bp Widom601 DNA


Mass: 36849.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PCR / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (120-MER) part of a full 147 bp Widom601 DNA


Mass: 37218.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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 complex of HHoB Asgard archaeal histone HHoB and DNA
Type: COMPLEX / Details: in presence of 1mM Mg / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.137 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, 1mM MgCl2
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESHEPES1
2100 mMSodium ChlorideNaCl1
31 mMMagnesium ChlorideMgCl21
SpecimenConc.: 0.192 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: 165000 X / Nominal defocus max: 1750 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: 59.4 e/Å2 / Film or detector model: TFS FALCON 4i (4k 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 selectionvia Topaz
7UCSF ChimeraX1.7.1model fittingRigid bod fit
9cryoSPARC4.4.1initial Euler assignmentAb-initio reconstruction
10cryoSPARC4.4.1final Euler assignmentNon-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 v1.7.1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3108514
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117260 / Details: in cryosparc / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / 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
21AOI

1aoi

I1AOII1-120DNA monomer2PDBexperimental model1-120
31AOI

1aoi

J1AOIJ172-292DNA monomer2PDBexperimental model172-292
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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