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PDB:1ZBB

Protein Name

Nucleosome (nucleosome core / DNA complex)

Species

Xenopus laevis (African clawed frog)

Biological Context

Compared with prokaryote DNA, eukaryote DNA are large in size, thereby it is necessary to fold highly. In case of human DNA, it is packed into nucleus of the cell with about 6 micrometer diameter, though it would extend about 2 meter if stretched out end to end. It is equivalent to packing a quite thin thread with 40 kilometer long into a teniss ball. Moreover, not only to pack DNA thickly but to pack regularly, the package system of chromatin must allow DNA repair enzyme and replicative enzyme to access when needed.

Structure Description

1zbb1zbb_x1zbb_y

For that purpose, eukaryote organisms fold their DNA into chromatin (30nm fiber), which consists of nucleus DNA and binding protein. If this chromatin is subjected to treatments that cause it to unfold partially, it can be seen under the electron microscope as a series of "beads on a string", which is called "nucleosome array". The string connecting each beads is called "linker DNA" consists of about 50 bp double strand DNA. And the beads is called "nucleosome core", which consists of core histon protein wrapped by 146 bp double strand DNA. The wrapping DNA turns about two times.

A nucleosome is the fundamental repeating element of nucleosome array, which consists of nucleosome core particle and exposed DNA between the nucleosome core particle called linker DNA. Although the structure of the nucleosome core is known at near atomic region, the organization of nucleosomes in the chromatin fibre is still controversial.

The structure shown here is that of the oligonucleosome (a compact tetranucleosome), solved by molecular replacement using the nucleosome core structure. DNA linker zigzags back and forth between two stacks of nucleosome cores. The authors propose continuous fibre models by successively stacking this tetranucleosomes one on another. The resulting models are nearly fully compacted and most closely resemble the previously described crossed-linker model in which nucleosomes are assembled in a zigzag ribbon that coils into a helix, rather than solenoid model in which a linear array of nucleosomes is coiled.

In addition, the figures shown below indicate a part of structure . In fig. 1, the half of nucleosome core including by one four kind of histone core proteins and a dsDNA. A nucleosome core has two structure shown fig. 1 piled up (see fig 2 and 3). The structure shown in this entry includes two nucleosome cores.

4_core_histon_and_dsDNA (Fig.1)A half of nucleosome core. Four kind of core histon proteins are surrounded by a dsDNA.
core_histon_and_dsDNA (Fig.2) The structure of nuleosome core. Two structure shown fig.1 are pilled up to this. Two this structure align and construct this entry.
core_histon_and_dsDNA (Fig.3) Shown from the right side of fig.2.

Protein Data Bank (PDB)

References

Source

  • Schalch, T. Duda, S. Sargent, D.F. Richmond, T.J.; "X-ray structure of a tetranucleosome and its implications for the chromatin fibre"; Nature; (2005) 436:138-141 PubMed:16001076

Others

author: Miho Higurashi


Japanese version:PDB:1ZBB