6YN1: Histone chaperone APLF acidic domain

Name: PDB 6YN1: Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer
Published: 2021-11-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer. Determined by X-ray diffraction at 2.35 Å resolution. Released 17 Nov 2021.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Xenopus laevis, Homo sapiens
Chains: 40
Atoms: 24,986
Mol. weight: 395.21 kDa
Released: 17 Nov 2021

Explore 6YN1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YN1 contains 153 α-helices and 103 β-strands across 40 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains a and Q: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	47
β-strand	55	1	45
α-helix	56-83	28
β-strand	88-89	2	46
α-helix	91-101	11
α-helix	104-122	19

Chains A and j: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	1
α-helix	46-72	27
β-strand	77-78	2	2
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	3

Chains b, C, g, H, l, M, R and W: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	43-56	14
α-helix	64-78	15
β-strand	83-84	2	4
α-helix	86-113	28
β-strand	118-119	2	5
α-helix	121-131	11

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-55	3	2
α-helix	56-83	28
β-strand	88-89	2	1
α-helix	91-101	11
α-helix	104-121	18

Chain c: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	5
α-helix	50-75	26
β-strand	80-81	2	4
α-helix	83-92	10
β-strand	96-98	3	40

Chains d, E, i, n, O, T and Y: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	469	1	4
α-helix	483	1
β-strand	484	1	41
α-helix	485	1

Chains D, h, I, m, N and S: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45-46	2	7
α-helix	50-75	26
β-strand	80-81	2	6
α-helix	83-92	10
β-strand	96-98	3	8

Chains e and U: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	10
α-helix	46-72	27
β-strand	77-78	2	11
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	12
α-helix	113-115	3

6 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H2A	A, F, K, P, U, Z, e, j	protein	107	Xenopus laevis	Q6AZJ8 (AlphaFold model)
Histone H2B	B, G, L, Q, V, a, f, k	protein	100	Xenopus laevis	P02281 (AlphaFold model)
Histone H3	C, H, M, R, W, b, g, l	protein	99	Xenopus laevis	P02302 (AlphaFold model)
Histone H4	D, I, N, S, X, c, h, m	protein	84	Xenopus laevis	P62799 (AlphaFold model)
Aprataxin and PNK-like factor	E, J, O, T, Y, d, i, n	protein	43	Homo sapiens	Q8IW19

Sequence of entity 1 (A, F, K, P, U, Z, e, j), FASTA

>6YN1_1 Histone H2A (chains A, F, K, P, U, Z, e, j)
MKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAAR
DNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK

Sequence of entity 2 (B, G, L, Q, V, a, f, k), FASTA

>6YN1_2 Histone H2B (chains B, G, L, Q, V, a, f, k)
MKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNK
RSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 3 (C, H, M, R, W, b, g, l), FASTA

>6YN1_3 Histone H3 (chains C, H, M, R, W, b, g, l)
MPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEAS
EAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 4 (D, I, N, S, X, c, h, m), FASTA

>6YN1_4 Histone H4 (chains D, I, N, S, X, c, h, m)
MKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKR
KTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (E, J, O, T, Y, d, i, n), FASTA

>6YN1_5 Aprataxin and PNK-like factor (chains E, J, O, T, Y, d, i, n)
GLDEDNDNVGQPNEYDLNDSFLDDEEEDYEPTDEDSDWEPGKE

Primary citation

Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF. Corbeski, I., Guo, X., Eckhardt, B.V. et al. Sci Adv (2022) 8:eabo0517-eabo0517. DOI 10.1126/sciadv.abo0517 · PubMed

Other PDB entries of the same protein (UniProt Q6AZJ8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
3MGR 2.3 Å, Binding of Rubidium ions to the Nucleosome Core Particle
8G86 2.3 Å, Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of…
8G88 2.3 Å, Human Oct4 bound to nucleosome with human nMatn1 sequence
9RXU 2.3 Å, RAPTA-C (Ruthenium[II]-cymene-phosphaadamantane) cancer drug binding to the nucleosome…
4KHA 2.35 Å, Structural basis of histone H2A-H2B recognition by the essential chaperone FACT
9WC0 2.4 Å, The structure of NCP-RA module of ncBAF-nucleosome complex
3MGP 2.44 Å, Binding of Cobalt ions to the Nucleosome Core Particle
3LZ0 2.5 Å, Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence…
3LZ1 2.5 Å, Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence…
9N6H 2.54 Å, 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex
9RXV 2.6 Å, RAPTA-T (Ruthenium[II]-toluene-phosphaadamantane) cancer drug binding to the nucleosome…

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