6YN1

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

PDB DOI: https://doi.org/10.2210/pdb6YN1/pdb

Classification: CHAPERONE
Organism(s): Xenopus laevis, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-10 Released: 2021-11-17
Deposition Author(s): Corbeski, I., Guo, X., Van Ingen, H., Sixma, T.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.233
R-Value Work: 0.177
R-Value Observed: 0.180

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

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.

(2022) Sci Adv 8: eabo0517-eabo0517

PubMed: 35895815 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abo0517
Primary Citation of Related Structures:
6YN1

PubMed Abstract:
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 (APLF ^AD) can assemble the histone octamer in a single step and deposit it on DNA to form nucleosomes. The crystal structure of the APLF ^AD-histone octamer complex shows that APLF ^AD tethers the histones in their nucleosomal conformation. Mutations of key aromatic anchor residues in APLF ^AD 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.

Organizational Affiliation

NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.

Macromolecule Content

Total Structure Weight: 395.21 kDa
Atom Count: 24,986
Modelled Residue Count: 3,071
Deposited Residue Count: 3,464
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	A EA [auth e] F JA [auth j] K A, EA [auth e], F, JA [auth j], K, P, U, Z	107	Xenopus laevis	Mutation(s): 0 Gene Names: hist1h2aj, h2ac14, LOC494591, XELAEV_18003602mg
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8 Go to UniProtKB: Q6AZJ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6AZJ8
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	AA [auth a] B FA [auth f] G KA [auth k] AA [auth a], B, FA [auth f], G, KA [auth k], L, Q, V	100	Xenopus laevis	Mutation(s): 0 Gene Names: XELAEV_18032685mg
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02281
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	BA [auth b] C GA [auth g] H LA [auth l] BA [auth b], C, GA [auth g], H, LA [auth l], M, R, W	99	Xenopus laevis	Mutation(s): 0 Gene Names: XELAEV_18002543mg
UniProt
Find proteins for P02302 (Xenopus laevis) Explore P02302 Go to UniProtKB: P02302
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02302
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	CA [auth c] D HA [auth h] I MA [auth m] CA [auth c], D, HA [auth h], I, MA [auth m], N, S, X	84	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62799
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Aprataxin and PNK-like factor	DA [auth d] E IA [auth i] J NA [auth n] DA [auth d], E, IA [auth i], J, NA [auth n], O, T, Y	43	Homo sapiens	Mutation(s): 0 Gene Names: APLF, C2orf13, PALF, XIP1 EC: 4.2.99.18 (PDB Primary Data), 3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IW19 (Homo sapiens) Explore Q8IW19 Go to UniProtKB: Q8IW19
PHAROS: Q8IW19 GTEx: ENSG00000169621
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IW19
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth h] SDF format, chain BB [auth j] SDF format, chain CB [auth j] SDF format, chain OA [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth H] SDF format, chain SA [auth K] SDF format, chain TA [auth N] SDF format, chain UA [auth P] SDF format, chain VA [auth S] SDF format, chain WA [auth U] SDF format, chain XA [auth b] SDF format, chain YA [auth c] SDF format, chain ZA [auth e] MOL2 format, chain AB [auth h] MOL2 format, chain BB [auth j] MOL2 format, chain CB [auth j] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth H] MOL2 format, chain SA [auth K] MOL2 format, chain TA [auth N] MOL2 format, chain UA [auth P] MOL2 format, chain VA [auth S] MOL2 format, chain WA [auth U] MOL2 format, chain XA [auth b] MOL2 format, chain YA [auth c] MOL2 format, chain ZA [auth e] mmCIF format, chain AB [auth h] mmCIF format, chain BB [auth j] mmCIF format, chain CB [auth j] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth H] mmCIF format, chain SA [auth K] mmCIF format, chain TA [auth N] mmCIF format, chain UA [auth P] mmCIF format, chain VA [auth S] mmCIF format, chain WA [auth U] mmCIF format, chain XA [auth b] mmCIF format, chain YA [auth c] mmCIF format, chain ZA [auth e]	AB [auth h] BB [auth j] CB [auth j] OA [auth A] PA [auth D] AB [auth h], BB [auth j], CB [auth j], OA [auth A], PA [auth D], QA [auth H], SA [auth K], TA [auth N], UA [auth P], VA [auth S], WA [auth U], XA [auth b], YA [auth c], ZA [auth e]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth h] Focus chain BB [auth j] Focus chain CB [auth j] Focus chain OA [auth A] Focus chain PA [auth D] Focus chain QA [auth H] Focus chain SA [auth K] Focus chain TA [auth N] Focus chain UA [auth P] Focus chain VA [auth S] Focus chain WA [auth U] Focus chain XA [auth b] Focus chain YA [auth c] Focus chain ZA [auth e] Interactions & Density Focus chain AB [auth h] Focus chain BB [auth j] Focus chain CB [auth j] Focus chain OA [auth A] Focus chain PA [auth D] Focus chain QA [auth H] Focus chain SA [auth K] Focus chain TA [auth N] Focus chain UA [auth P] Focus chain VA [auth S] Focus chain WA [auth U] Focus chain XA [auth b] Focus chain YA [auth c] Focus chain ZA [auth e]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain RA [auth J] MOL2 format, chain RA [auth J] mmCIF format, chain RA [auth J]	RA [auth J]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain RA [auth J] Interactions & Density Focus chain RA [auth J]