1ZBB

Structure of the 4_601_167 Tetranucleosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 9 Å
  • R-Value Work: 0.386 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray structure of a tetranucleosome and its implications for the chromatin fibre.

Schalch, T.Duda, S.Sargent, D.F.Richmond, T.J.

(2005) Nature 436: 138-141

  • DOI: 10.1038/nature03686

  • PubMed Abstract: 
  • DNA in eukaryotic chromosomes is organized in arrays of nucleosomes compacted into chromatin fibres. This higher-order structure of nucleosomes is the substrate for DNA replication, recombination, transcription and repair. Although the structure of t ...

    DNA in eukaryotic chromosomes is organized in arrays of nucleosomes compacted into chromatin fibres. This higher-order structure of nucleosomes is the substrate for DNA replication, recombination, transcription and repair. Although the structure of the nucleosome core is known at near-atomic resolution, even the most fundamental information about the organization of nucleosomes in the fibre is controversial. Here we report the crystal structure of an oligonucleosome (a compact tetranucleosome) at 9 A resolution, solved by molecular replacement using the nucleosome core structure. The structure shows that linker DNA zigzags back and forth between two stacks of nucleosome cores, which form a truncated two-start helix, and does not follow a path compatible with a one-start solenoidal helix. The length of linker DNA is most probably buffered by stretching of the DNA contained in the nucleosome cores. We have built continuous fibre models by successively stacking tetranucleosomes one on another. The resulting models are nearly fully compacted and most closely resemble the previously described crossed-linker model. They suggest that the interfaces between nucleosomes along a single helix start are polymorphic.


    Organizational Affiliation

    ETH Zürich, Institute for Molecular Biology and Biophysics, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HISTONE H3
A, E, a, e
135Xenopus laevis
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F, b, f
102Xenopus laevis
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2A.1
C, G, c, g
129Xenopus laevis
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Histone H2B.1
D, H, d, h
125Xenopus laevis
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 1
MoleculeChainsLengthOrganism
DNA STRAND 1 (ARBITRARY MODEL SEQUENCE)I347N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA STRAND 2 (ARBITRARY MODEL SEQUENCE)J347N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 9 Å
  • R-Value Work: 0.386 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 127.675α = 90.00
b = 168.445β = 90.00
c = 237.126γ = 90.00
Software Package:
Software NamePurpose
BEASTphasing
REFMACrefinement
BEASTmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-05-14
    Type: Other