[English] 日本語
Yorodumi
- PDB-9qv7: Asgard HHoB nucleosome in the open state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qv7
TitleAsgard HHoB nucleosome in the open state
Components
  • (DNA (120-MER) from Widom601) x 2
  • Archaeal histone A
KeywordsDNA BINDING PROTEIN / archaea / chromatin / histone / DNA / Asgard / 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: 3.6 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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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) from Widom601
Y: DNA (120-MER) from Widom601


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

-
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) from Widom601


Mass: 36849.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: produced by PCR / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (120-MER) from Widom601


Mass: 37218.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: produced by PCR / Source: (synth.) synthetic construct (others)
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Open complex of HHoB Asgard archaeal histone and DNA / Type: COMPLEX
Details: Open state of the HHoB nucleosome, reconstituted in vitro
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) / Plasmid: LIC-1B
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 / Details: 20 mM HEPES pH 7.5, 100 mM NaCl, 1mM MgCl2
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

-
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: 59.44 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

-
Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4.1particle selectionvia Topaz
2SerialEMimage acquisition
7UCSF ChimeraX1.7.1model fittingRigid body fit
9PHENIX1.21.1model refinementReal space refinement
10Coot0.9.8.93model refinementResidue fitting with helical and DNA-B form restraints
11UCSF ChimeraX1.7.1model refinementRelaxation into density using ISOLDE
12cryoSPARC4.4.1initial Euler assignmentAb-initio reconstruction
13cryoSPARC4.4.1final Euler assignmentNon-uniform refinement
15cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3108514
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96738 / Algorithm: FOURIER SPACE / 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 predication of HHoB1AlphaFoldin silico model
27X58

7x58

I7X58I1-120DNA monomer2PDBexperimental model1-120
37X58

7x58

J7X58J-59-0DNA monomer2PDBexperimental model-59-0
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more