9QV6 | pdb_00009qv6

Asgard HHoB hypernucleosome in the closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM reveals open and closed Asgard chromatin assemblies.

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

(2025) Mol Cell 85: 4152

  • DOI: https://doi.org/10.1016/j.molcel.2025.10.001
  • Primary Citation of Related Structures:  
    9QV5, 9QV6, 9QV7

  • PubMed 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, 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.


  • Organizational Affiliation
    • Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Archaeal histone A
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
71Candidatus Heimdallarchaeota archaeon LC_3Mutation(s): 0 
Gene Names: HeimC3_17480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (180-MER)M [auth X]180synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (180-MER)N [auth Y]180synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1
MODEL REFINEMENTPHENIX1.21.1
MODEL REFINEMENTCoot0.9.8.93
MODEL REFINEMENTUCSF ChimeraX1.7,1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union3DchromArchaea 101076671

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Data collection, Database references
  • Version 1.2: 2025-11-12
    Changes: Data collection, Database references
  • Version 1.3: 2025-12-03
    Changes: Data collection, Database references