6KXV image
Deposition Date 2019-09-13
Release Date 2020-07-22
Last Version Date 2023-11-22
Entry Detail
PDB ID:
6KXV
Title:
Crystal structure of a nucleosome containing Leishmania histone H3
Biological Source:
Source Organism:
Leishmania major (Taxon ID: 5664)
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.63 Å
R-Value Free:
0.26
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Histone H3
Gene (Uniprot):LMJF_10_0870, LMJF_10_0990, LMJF_16_0570, LMJF_16_0575, LMJF_16_0610
Chain IDs:A, E
Chain Length:133
Number of Molecules:2
Biological Source:Leishmania major
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
Chain Length:106
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-B/E
Gene (Uniprot):H2AC4, H2AC8
Chain IDs:C, G
Chain Length:133
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-J
Gene (Uniprot):H2BC11
Chain IDs:D, H
Chain Length:129
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (146-MER)
Chain IDs:I, J
Chain Length:146
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Incorporation and influence of Leishmania histone H3 in chromatin.
Nucleic Acids Res. 47 11637 11648 (2019)
PMID: 31722422 DOI: 10.1093/nar/gkz1040

Abstact

Immunopathologies caused by Leishmania cause severe human morbidity and mortality. This protozoan parasite invades and persists inside host cells, resulting in disease development. Leishmania modifies the epigenomic status of the host cells, thus probably averting the host cell defense mechanism. To accomplish this, Leishmania may change the host cell chromatin structure. However, the mechanism by which the parasite changes the host cell chromatin has not been characterized. In the present study, we found that ectopically produced Leishmania histone H3, LmaH3, which mimics the secreted LmaH3 in infected cells, is incorporated into chromatin in human cells. A crystallographic analysis revealed that LmaH3 forms nucleosomes with human histones H2A, H2B and H4. We found that LmaH3 was less stably incorporated into the nucleosome, as compared to human H3.1. Consistently, we observed that LmaH3-H4 association was remarkably weakened. Mutational analyses revealed that the specific LmaH3 Trp35, Gln57 and Met98 residues, which correspond to the H3.1 Tyr41, Arg63 and Phe104 residues, might be responsible for the instability of the LmaH3 nucleosome. Nucleosomes containing LmaH3 resisted the Mg2+-mediated compaction of the chromatin fiber. These distinct physical characteristics of LmaH3 support the possibility that histones secreted by parasites during infection may modulate the host chromatin structure.

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Disease

Primary Citation of related structures