1id3 Summary

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CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS

The structure was published by White, C.L., Suto, R.K., and Luger, K., in 2001 in a paper entitled "Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 3.1 Å and deposited in 2001.

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

This entry contains 37 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 P61830 (2-136) (H3_YEAST)search Saccharomyces cerevisiae S288csearch 99% 135 71%
E HISTONE H3 P61830 (2-136) (H3_YEAST)search Saccharomyces cerevisiae S288csearch 99% 135 71%
B HISTONE H4 P02309 (2-103) (H4_YEAST)search Saccharomyces cerevisiae S288csearch 99% 102 83%
F HISTONE H4 P02309 (2-103) (H4_YEAST)search Saccharomyces cerevisiae S288csearch 99% 102 83%
C HISTONE H2A.1 P04911 (2-132) (H2A1_YEAST)search Saccharomyces cerevisiae S288csearch 99% 131 83%
G HISTONE H2A.1 P04911 (2-132) (H2A1_YEAST)search Saccharomyces cerevisiae S288csearch 99% 131 83%
D HISTONE H2B.2 P02294 (2-131) (H2B2_YEAST)search Saccharomyces cerevisiae S288csearch 99% 130 73%
H HISTONE H2B.2 P02294 (2-131) (H2B2_YEAST)search Saccharomyces cerevisiae S288csearch 99% 130 73%


This entry contains 4 unique UniProt proteins:

UniProt accession Name Organism PDB
P61830 (2 - 136) HISTONE H3 Saccharomyces cerevisiae
P02309 (2 - 103) HISTONE H4 Saccharomyces cerevisiae
P04911 (2 - 132) HISTONE H2A.1 Saccharomyces cerevisiae
P02294 (2 - 131) HISTONE H2B.2 Saccharomyces cerevisiae

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A, E (P61830) Nucleosome core histonessearch Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search
B, F (P02309) Nucleosome core histonessearch Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search
C, G (P04911) Nucleosome core histonessearch Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search
D, H (P02294) Nucleosome core histonessearch Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search

Chain ID Cellular component (GO) Molecular function (GO) Biological process (GO)
A, E (P61830) nucleosomesearch nucleussearch chromosomesearch CENP-A containing nucleosomesearch replication fork protection complexsearch nuclear nucleosomesearch DNA bindingsearch protein heterodimerization activitysearch protein bindingsearch mitotic spindle assembly checkpointsearch sexual sporulation resulting in formation of a cellular sporesearch global genome nucleotide-excision repairsearch chromatin assembly or disassemblysearch rRNA transcriptionsearch
B, F (P02309) nucleussearch nucleosomesearch replication fork protection complexsearch chromosomesearch nuclear nucleosomesearch DNA bindingsearch protein bindingsearch protein heterodimerization activitysearch nucleosome assemblysearch sexual sporulation resulting in formation of a cellular sporesearch histone H3-K79 methylationsearch transfer RNA gene-mediated silencingsearch chromatin assembly or disassemblysearch
C, G (P04911) nucleosomesearch nucleussearch replication fork protection complexsearch nuclear nucleosomesearch chromosomesearch protein heterodimerization activitysearch DNA bindingsearch transfer RNA gene-mediated silencingsearch DNA repairsearch cellular response to DNA damage stimulussearch chromatin assembly or disassemblysearch negative regulation of transcription from RNA polymerase II promotersearch
D, H (P02294) nucleosomesearch nucleussearch nuclear nucleosomesearch chromosomesearch replication fork protection complexsearch protein heterodimerization activitysearch DNA bindingsearch protein bindingsearch chromatin assembly or disassemblysearch

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