6L4A image
Deposition Date 2019-10-16
Release Date 2019-12-04
Last Version Date 2024-03-27
Entry Detail
PDB ID:
6L4A
Keywords:
NUCLEAR PROTEIN
Title:
H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
12.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6L4A validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.1
Gene (Uniprot):H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12
Chain IDs:A, E, K, O, S, W
Chain Length:139
Number of Molecules:6
Biological Source:Homo sapiens
UniProt ID:P68431 Pfam ID:PF00125
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16
Chain IDs:B, F, L, P, T, X
Chain Length:106
Number of Molecules:6
Biological Source:Homo sapiens
UniProt ID:P62805 Pfam ID:PF15511
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-B/E
Gene (Uniprot):H2AC4, H2AC8
Chain IDs:C, G, M, Q, U, Y
Chain Length:133
Number of Molecules:6
Biological Source:Homo sapiens
UniProt ID:P04908 Pfam ID:PF00125, PF16211
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-J
Gene (Uniprot):H2BC11
Chain IDs:D, H, N, R, V, Z
Chain Length:129
Number of Molecules:6
Biological Source:Homo sapiens
UniProt ID:P06899 Pfam ID:PF00125
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (485-MER)
Chain IDs:I
Chain Length:485
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (485-MER)
Chain IDs:J
Chain Length:485
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
NA
Primary Citation
Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome.
Structure 28 44 ? (2020)
PMID: 31711756 DOI: 10.1016/j.str.2019.10.016

Abstact

The histone H3 variant CENP-A is a crucial epigenetic marker for centromere specification. CENP-A forms a characteristic nucleosome and dictates the higher-order configuration of centromeric chromatin. However, little is known about how the CENP-A nucleosome affects the architecture of centromeric chromatin. In this study, we reconstituted tri-nucleosomes mimicking a centromeric nucleosome arrangement containing the CENP-A nucleosome, and determined their 3D structures by cryoelectron microscopy. The H3-CENP-A-H3 tri-nucleosomes adopt an untwisted architecture, with an outward-facing linker DNA path between nucleosomes. This is distinct from the H3-H3-H3 tri-nucleosome architecture, with an inward-facing DNA path. Intriguingly, the untwisted architecture may allow the CENP-A nucleosome to be exposed to the solvent in the condensed chromatin model. These results provide a structural basis for understanding the 3D configuration of CENP-A-containing chromatin, and may explain how centromeric proteins can specifically target the CENP-A nucleosomes buried in robust amounts of H3 nucleosomes in centromeres.

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Primary Citation of related structures
6L4A