2nzd Summary

pdbe.org/2nzd
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Nucleosome core particle containing 145 bp of DNA

The structure was published by Ong, M.S., Richmond, T.J., and Davey, C.A., in 2007 in a paper entitled "DNA stretching and extreme kinking in the nucleosome core" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.65 Å and deposited in 2006.

The experimental data on which the structure is based was also deposited.

This entry contains 31 copies of 6 unique biopolymers (complete list).

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterodecamers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Histone H3 P84233 (2-136) (H32_XENLA)search Xenopus laevissearch 99% 135 71%
E Histone H3 P84233 (2-136) (H32_XENLA)search Xenopus laevissearch 99% 135 71%
B Histone H4 P62799 (2-103) (H4_XENLA)search Xenopus laevissearch 99% 102 85%
F Histone H4 P62799 (2-103) (H4_XENLA)search Xenopus laevissearch 99% 102 85%
C histone H2A P06897 (2-120) (H2A1_XENLA)search Xenopus laevissearch 92% 119 89%
G histone H2A P06897 (2-120) (H2A1_XENLA)search Xenopus laevissearch 92% 119 89%
D Histone H2B P02281 (2-126) (H2B11_XENLA)search Xenopus laevissearch 97% 125 76%
H Histone H2B P02281 (2-126) (H2B11_XENLA)search Xenopus laevissearch 97% 125 76%


This entry contains 4 unique UniProt proteins:

UniProt accession Name Organism PDB
P84233 (2 - 136) Histone H3 Xenopus laevis
P62799 (2 - 103) Histone H4 Xenopus laevis
P06897 (2 - 120) histone H2A Xenopus laevis
P02281 (2 - 126) Histone H2B Xenopus laevis

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A, E (P84233) Nucleosome core histonessearch Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search
B, F (P62799) Nucleosome core histonessearch Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search
C, G (P06897) Nucleosome core histonessearch Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search
D, H (P02281) Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search

Chain ID Cellular component (GO) Molecular function (GO) Biological process (GO)
A, E (P84233) nucleosomesearch nucleussearch chromosomesearch nucleoplasmsearch protein bindingsearch protein heterodimerization activitysearch DNA bindingsearch
B, F (P62799) nucleosomesearch nucleussearch chromosomesearch protein heterodimerization activitysearch DNA bindingsearch protein bindingsearch DNA-templated transcription, initiationsearch nucleosome assemblysearch
C, G (P06897) nucleussearch chromosomesearch nucleosomesearch protein heterodimerization activitysearch DNA bindingsearch
D, H (P02281) nucleussearch nucleosomesearch chromosomesearch DNA bindingsearch protein heterodimerization activitysearch

Chain InterPro annotation
A, E Histone H3/CENP-Asearch Histone coresearch Histone-foldsearch
B, F Histone H4search Histone coresearch Histone-foldsearch Histone H4, conserved sitesearch
C, G Histone H2Asearch Histone coresearch Histone-foldsearch
D, H Histone H2Bsearch Histone coresearch Histone-foldsearch