1f66 Summary

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2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z

The structure was published by Suto, R.K., Clarkson, M.J., Tremethick, D.J., and Luger, K., in 2000 in a paper entitled "Crystal structure of a nucleosome core particle containing the variant histone H2A.Z." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.6 Å and deposited in 2000.

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

This entry contains 35 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 P84233 (1-136) (H32_XENLA)search Xenopus laevissearch 99% 136 75%
E HISTONE H3 P84233 (1-136) (H32_XENLA)search Xenopus laevissearch 99% 136 75%
B HISTONE H4 P62806 (1-103) (H4_MOUSE)search Mus musculussearch 100% 103 83%
F HISTONE H4 P62806 (1-103) (H4_MOUSE)search Mus musculussearch 100% 103 83%
C HISTONE H2A.Z P0C0S5 (1-128) (H2AZ_HUMAN)search Homo sapienssearch 100% 128 83%
G HISTONE H2A.Z P0C0S5 (1-128) (H2AZ_HUMAN)search Homo sapienssearch 100% 128 83%
D HISTONE H2B P02281 (1-126) (H2B11_XENLA)search Xenopus laevissearch 97% 126 75%
H HISTONE H2B P02281 (1-126) (H2B11_XENLA)search Xenopus laevissearch 97% 126 75%


This entry contains 4 unique UniProt proteins:

UniProt accession Name Organism PDB
P84233 (1 - 136) HISTONE H3 Xenopus laevis
P62806 (1 - 103) HISTONE H4 Mus musculus
P0C0S5 (1 - 128) HISTONE H2A.Z Homo sapiens
P02281 (1 - 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 (P62806) Nucleosome core histonessearch Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search
C, G (P0C0S5) 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 nucleussearch chromosomesearch nucleoplasmsearch
B, F (P62806) protein heterodimerization activitysearch DNA bindingsearch protein bindingsearch poly(A) RNA bindingsearch nucleussearch nucleosomesearch protein complexsearch nucleoplasmsearch membranesearch chromosomesearch extracellular exosomesearch nuclear chromosomesearch nucleosome assemblysearch DNA-templated transcription, initiationsearch negative regulation of megakaryocyte differentiationsearch DNA replication-dependent nucleosome assemblysearch DNA replication-independent nucleosome assemblysearch chromatin silencing at rDNAsearch
C, G (P0C0S5) DNA bindingsearch protein heterodimerization activitysearch nucleosomal DNA bindingsearch protein bindingsearch RNA polymerase II core promoter sequence-specific DNA bindingsearch RNA polymerase II distal enhancer sequence-specific DNA bindingsearch chromatin DNA bindingsearch RNA polymerase II core promoter proximal region sequence-specific DNA bindingsearch nucleosomesearch nucleussearch chromosomesearch nuclear heterochromatinsearch nuclear euchromatinsearch extracellular exosomesearch Barr bodysearch positive regulation of transcription from RNA polymerase II promotersearch cellular response to estradiol stimulussearch
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