2cv5 Summary

pdbe.org/2cv5
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Crystal structure of human nucleosome core particle

The structure was published by Tsunaka, Y., Kajimura, N., Tate, S., and Morikawa, K., in 2005 in a paper entitled "Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.5 Å and deposited in 2005.

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

This entry contains 33 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 H3.1 P68431 (1-136) (H31_HUMAN)search Homo sapienssearch 100% 136 72%
E Histone H3.1 P68431 (1-136) (H31_HUMAN)search Homo sapienssearch 100% 136 72%
B Histone H4 P62805 (1-103) (H4_HUMAN)search Homo sapienssearch 99% 103 82%
F Histone H4 P62805 (1-103) (H4_HUMAN)search Homo sapienssearch 99% 103 82%
C Histone H2A.a P04908 (1-130) (H2A1B_HUMAN)search Homo sapienssearch 92% 130 83%
G Histone H2A.a P04908 (1-130) (H2A1B_HUMAN)search Homo sapienssearch 92% 130 83%
D Histone H2B K O60814 (1-126) (H2B1K_HUMAN)search Homo sapienssearch 100% 126 76%
H Histone H2B K O60814 (1-126) (H2B1K_HUMAN)search Homo sapienssearch 100% 126 76%


This entry contains 4 unique UniProt proteins:

UniProt accession Name Organism PDB
P68431 (1 - 136) Histone H3.1 Homo sapiens
P62805 (1 - 103) Histone H4 Homo sapiens
P04908 (1 - 130) Histone H2A.a Homo sapiens
O60814 (1 - 126) Histone H2B K Homo sapiens

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A, E (P68431) Nucleosome core histonessearch Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search
B, F (P62805) Nucleosome core histonessearch Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search
C, G (P04908) Nucleosome core histonessearch Histone, subunit Asearch PF00125: Core histone H2A/H2B/H3/H4search
D, H (O60814) 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 (P68431) DNA bindingsearch protein heterodimerization activitysearch protein bindingsearch nucleosomesearch nucleoplasmsearch membranesearch extracellular vesicular exosomesearch protein complexsearch nucleussearch extracellular regionsearch chromosomesearch nuclear chromosomesearch DNA replication-dependent nucleosome assemblysearch regulation of gene silencingsearch chromatin organizationsearch blood coagulationsearch
B, F (P62805) DNA bindingsearch protein heterodimerization activitysearch protein bindingsearch poly(A) RNA bindingsearch histone demethylase activity (H4-K20 specific)search nucleosomesearch nucleussearch nucleoplasmsearch protein complexsearch nuclear chromosomesearch extracellular vesicular exosomesearch extracellular regionsearch chromosomesearch membranesearch nucleosome assemblysearch CENP-A containing nucleosome assemblysearch histone H4-K20 demethylationsearch DNA replication-independent nucleosome assemblysearch mitotic cell cyclesearch DNA replication-dependent nucleosome assemblysearch telomere maintenancesearch chromatin organizationsearch negative regulation of megakaryocyte differentiationsearch
C, G (P04908) DNA bindingsearch protein heterodimerization activitysearch nucleussearch nucleosomesearch extracellular vesicular exosomesearch chromosomesearch biological_processsearch
D, H (O60814) protein heterodimerization activitysearch DNA bindingsearch molecular_functionsearch nucleosomesearch nucleussearch extracellular spacesearch chromosomesearch nucleoplasmsearch antibacterial humoral responsesearch chromatin organizationsearch defense response to bacteriumsearch innate immune response in mucosasearch defense response to Gram-positive bacteriumsearch

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