1m1a Summary

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LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

The structure was published by Suto, R.K., Edayathumangalam, R.S., White, C.L., et al., Gottesfeld, J.M., Dervan, P.B., and Luger, K., in 2003 in a paper entitled "Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.65 Å and deposited in 2002.

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

This entry contains 31 copies of 5 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 H3.2 P02302 (2-136) (H3C_XENLA)search Xenopus laevissearch 99% 135 73%
E Histone H3.2 P02302 (2-136) (H3C_XENLA)search Xenopus laevissearch 99% 135 73%
B Histone H4 P62799 (2-103) (H4_XENLA)search Xenopus laevissearch 99% 102 91%
F Histone H4 P62799 (2-103) (H4_XENLA)search Xenopus laevissearch 99% 102 91%
C Histone H2A.1 P06897 (2-130) (H2A1_XENLA)search Xenopus laevissearch 92% 129 82%
G Histone H2A.1 P06897 (2-130) (H2A1_XENLA)search Xenopus laevissearch 92% 129 82%
D Histone H2B.1 P02281 (2-126) (H2B11_XENLA)search Xenopus laevissearch 97% 125 74%
H Histone H2B.1 P02281 (2-126) (H2B11_XENLA)search Xenopus laevissearch 97% 125 74%


This entry contains 4 unique UniProt proteins:

UniProt accession Name Organism PDB
P02302 (2 - 136) Histone H3.2 Xenopus laevis
P62799 (2 - 103) Histone H4 Xenopus laevis
P06897 (2 - 130) Histone H2A.1 Xenopus laevis
P02281 (2 - 126) Histone H2B.1 Xenopus laevis

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A, E (P02302) 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 (P02302) DNA bindingsearch protein heterodimerization activitysearch nucleosomesearch nucleussearch chromosomesearch
B, F (P62799) protein heterodimerization activitysearch DNA bindingsearch protein bindingsearch nucleussearch chromosomesearch nucleosomesearch nucleosome assemblysearch
C, G (P06897) DNA bindingsearch protein heterodimerization activitysearch nucleosomesearch nucleussearch chromosomesearch
D, H (P02281) DNA bindingsearch protein heterodimerization activitysearch nucleussearch nucleosomesearch 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