ISDA

Deposition Date 2020-04-10

Release Date 2021-11-17

Last Version Date 2024-01-24

Entry Detail

PDB ID:

6YN1

Keywords:

CHAPERONE

Title:

Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer

Biological Source:

Source Organism:

Xenopus laevis (Taxon ID: 8355)
Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.35 Å

R-Value Free:

0.23

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2A
Gene (Uniprot):LOC494591
Chain IDs:A, F, K, P, U, Z, EA (auth: e), JA (auth: j)
Chain Length:107
Number of Molecules:8
Biological Source:Xenopus laevis

UniProt ID:Q6AZJ8 Pfam ID:PF00125, PF16211

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2B
Chain IDs:B, G, L, Q, V, AA (auth: a), FA (auth: f), KA (auth: k)
Chain Length:107
Number of Molecules:8
Biological Source:Xenopus laevis

UniProt ID:P02281 Pfam ID:PF00125

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3
Chain IDs:C, H, M, R, W, BA (auth: b), GA (auth: g), LA (auth: l)
Chain Length:99
Number of Molecules:8
Biological Source:Xenopus laevis

UniProt ID:P02302 Pfam ID:PF00125

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:D, I, N, S, X, CA (auth: c), HA (auth: h), MA (auth: m)
Chain Length:84
Number of Molecules:8
Biological Source:Xenopus laevis

UniProt ID:P62799 Pfam ID:PF15511

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Aprataxin and PNK-like factor
Gene (Uniprot):APLF
Chain IDs:E, J, O, T, Y, DA (auth: d), IA (auth: i), NA (auth: n)
Chain Length:84
Number of Molecules:8
Biological Source:Homo sapiens

UniProt ID:Q8IW19

Ligand Molecules

GOL

Primary Citation

Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF.

Corbeski, I, Guo, X, Eckhardt, B.V, Fasci, D, Wiegant, W, Graewert, M.A, Vreeken, K, Wienk, H, Svergun, D.I, Heck, A.J.R, van Attikum, H, Boelens, R, Sixma, T.K, Mattiroli, F, van Ingen, H.Show

Sci Adv 8 eabo0517 eabo0517 (2022)

PMID: 35895815 DOI: 10.1126/sciadv.abo0517

Abstact

Nucleosome assembly requires the coordinated deposition of histone complexes H3-H4 and H2A-H2B to form a histone octamer on DNA. In the current paradigm, specific histone chaperones guide the deposition of first H3-H4 and then H2A-H2B. Here, we show that the acidic domain of DNA repair factor APLF (APLFAD) can assemble the histone octamer in a single step and deposit it on DNA to form nucleosomes. The crystal structure of the APLFAD-histone octamer complex shows that APLFAD tethers the histones in their nucleosomal conformation. Mutations of key aromatic anchor residues in APLFAD affect chaperone activity in vitro and in cells. Together, we propose that chaperoning of the histone octamer is a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted.

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Primary Citation of related structures