3c1c Summary

pdbe.org/3c1c
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The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure

The structure was published by Lu, X., Simon, M.D., Chodaparambil, J.V., Hansen, J.C., Shokat, K.M., and Luger, K., in 2008 in a paper entitled "The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 3.15 Å and deposited in 2008.

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

This entry contains 20 copies of 5 unique biopolymers (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-like P84233 (2-136) (H32_XENLA)search Xenopus laevissearch 99% 135 72%
E Histone H3-like P84233 (2-136) (H32_XENLA)search Xenopus laevissearch 99% 135 72%
B Histone H4 P62799 (2-103) (H4_XENLA)search Xenopus laevissearch 99% 102 82%
F Histone H4 P62799 (2-103) (H4_XENLA)search Xenopus laevissearch 99% 102 82%
C Histone H2A type 1 P06897 (2-130) (H2A1_XENLA)search Xenopus laevissearch 92% 129 81%
G Histone H2A type 1 P06897 (2-130) (H2A1_XENLA)search Xenopus laevissearch 92% 129 81%
D Histone 2, H2bf Q28D68 (2-126) (Q28D68_XENTR)search Xenopus (Silurana) tropicalissearch 99% 125 74%
H Histone 2, H2bf Q28D68 (2-126) (Q28D68_XENTR)search Xenopus (Silurana) tropicalissearch 99% 125 74%


This entry contains 4 unique UniProt proteins:

UniProt accession Name Organism PDB
P84233 (2 - 136) Histone H3-like Xenopus laevis
P62799 (2 - 103) Histone H4 Xenopus laevis
P06897 (2 - 130) Histone H2A type 1 Xenopus laevis
Q28D68 (2 - 126) Histone 2, H2bf Xenopus (Silurana) tropicalis

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A, E (P84233) 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 (Q28D68) 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 bindingsearch DNA bindingsearch protein heterodimerization activitysearch nucleussearch nucleosomesearch chromosomesearch nucleoplasmsearch
B, F (P62799) protein bindingsearch DNA bindingsearch protein heterodimerization activitysearch nucleussearch nucleosomesearch chromosomesearch nucleosome assemblysearch DNA-templated transcription, initiationsearch
C, G (P06897) DNA bindingsearch protein heterodimerization activitysearch chromosomesearch nucleussearch nucleosomesearch
D, H (Q28D68) DNA bindingsearch protein heterodimerization activitysearch chromosomesearch nucleosomesearch nucleussearch

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