5T5K

Structure of histone-based chromatin in Archaea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1126/science.aaj1849

  • 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, i ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-binding protein HMf-2
A, B, C, D, E, F
69Methanothermus fervidusMutation(s): 0 
Gene Names: hmfB
Find proteins for P19267 (Methanothermus fervidus)
Go to UniProtKB:  P19267
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (90-MER)I90synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (90-MER)J90synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

Download SDF File 
Download CCD File 
B, D, F
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 99.454α = 90.00
b = 99.454β = 90.00
c = 171.730γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM 067777
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM53185

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release