1kx5 Summary

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X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution

The structure was published by Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., and Richmond, T.J., in 2002 in a paper entitled "Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.94 Å and deposited in 2002.

The experimental data on which the structure is based was not deposited.

This entry contains 38 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% 135 100%
E histone H3 P84233 (2-136) (H32_XENLA)search Xenopus laevissearch 99% 135 100%
B histone H4 P62799 (2-103) (H4_XENLA)search Xenopus laevissearch 99% 102 100%
F histone H4 P62799 (2-103) (H4_XENLA)search Xenopus laevissearch 99% 102 100%
C histone H2A.1 P06897 (2-130) (H2A1_XENLA)search Xenopus laevissearch 92% 128 100%
G histone H2A.1 P06897 (2-130) (H2A1_XENLA)search Xenopus laevissearch 92% 128 100%
D histone H2B.2 P02281 (2-126) (H2B11_XENLA)search Xenopus laevissearch 97% 125 97%
H histone H2B.2 P02281 (2-126) (H2B11_XENLA)search Xenopus laevissearch 97% 125 97%


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 - 130) histone H2A.1 Xenopus laevis
P02281 (2 - 126) histone H2B.2 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) Nucleosome core histonessearch Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search

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

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