5T5K

Structure of histone-based chromatin in Archaea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of histone-based chromatin in Archaea.

Mattiroli, F.Bhattacharyya, S.Dyer, P.N.White, A.E.Sandman, K.Burkhart, B.W.Byrne, K.R.Lee, T.Ahn, N.G.Santangelo, T.J.Reeve, J.N.Luger, K.

(2017) Science 357: 609-612

  • DOI: https://doi.org/10.1126/science.aaj1849
  • Primary Citation of Related Structures:  
    5T5K

  • PubMed Abstract: 

    Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix with the same geometry as DNA in the eukaryotic nucleosome. Substitutions of a conserved glycine at the interface of adjacent protein layers destabilize archaeal chromatin, reduce growth rate, and impair transcription regulation, confirming the biological importance of the polymeric structure. Our data establish that the histone-based mechanism of DNA compaction predates the nucleosome, illuminating the origin of the nucleosome.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-binding protein HMf-2
A, B, C, D, E
A, B, C, D, E, F
69Methanothermus fervidusMutation(s): 0 
Gene Names: hmfB
UniProt
Find proteins for P19267 (Methanothermus fervidus)
Explore P19267 
Go to UniProtKB:  P19267
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19267
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (90-MER)G [auth I]90synthetic construct
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (90-MER)H [auth J]90synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.454α = 90
b = 99.454β = 90
c = 171.73γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM 067777
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM53185

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description