5JA4: Histone H3.3

Crystal structure of human TONSL and MCM2 HBDs binding to a histone H3-H4 tetramer. Determined by X-ray diffraction at 2.42 Å resolution. Released 15 Jun 2016.

Method: X-ray diffraction
Resolution: 2.42 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,019
Mol. weight: 48.9 kDa
Released: 15 Jun 2016

Explore 5JA4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JA4 contains 20 α-helices and 6 β-strands across 4 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.

Chain A: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-130	10

Chain B: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-19	3
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	70-71	2	2
α-helix	77-81	5
β-strand	95	1	1
α-helix	103-106	4
α-helix	107-122	16

Chain D: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	532-539	8
α-helix	542-551	10
α-helix	565-572	8
α-helix	575-583	9
α-helix	592-593	2
α-helix	601-607	7
α-helix	611-616	6
α-helix	634-644	11
α-helix	651-668	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.3	A	protein	79	Homo sapiens	P84243 (AlphaFold model)
Histone H4	B	protein	102	Homo sapiens	P62805 (AlphaFold model)
DNA replication licensing factor MCM2	C	protein	70	Homo sapiens	P49736 (AlphaFold model)
Tonsoku-like protein	D	protein	181	Homo sapiens	Q96HA7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5JA4_1 Histone H3.3 (chains A)
STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA

Sequence of entity 2 (B), FASTA

>5JA4_2 Histone H4 (chains B)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C), FASTA

>5JA4_3 DNA replication licensing factor MCM2 (chains C)
GPLEEEEDGEELIGDGMERDYRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQR
DREAGRGLGR

Sequence of entity 4 (D), FASTA

>5JA4_4 Tonsoku-like protein (chains D)
GHLGRRKGSKWNRRNDMGETLLHRACIEGQLRRVQDLVRQGHPLNPRDYCGWTPLHEACN
YGHLEIVRFLLDHGAAVDDPGGQGCEGITPLHDALNCGHFEVAELLLERGASVTLRTRKG
LSPLETLQQWVKLYRRDLDLETRQKARAMEMLLQAAASGQDPHSSQAFHTPSSLLFDPET
S

Primary citation

H4K20me0 marks post-replicative chromatin and recruits the TONSL-MMS22L DNA repair complex. Saredi, G., Huang, H., Hammond, C.M. et al. Nature (2016) 534:714-718. DOI 10.1038/nature18312 · PubMed

Other PDB entries of the same protein (UniProt P84243 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3QL9 0.93 Å, Monoclinic complex structure of ATRX ADD bound to histone H3K9me3 peptide
4GNE 1.47 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7
4L58 1.48 Å, Crystal structure of the MLL5 PHD finger in complex with H3K4me3
5JLB 1.5 Å, Crystal structure of SETD2 bound to histone H3.3 K36I peptide
4GNF 1.55 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15
3QLA 1.6 Å, Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide
3MUL 1.65 Å, Crystal structure of Brd4 bromodomain 1 with butyrylated histone H3-K(buty)14
9G4A 1.65 Å, Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide
4GNG 1.73 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide
3MUK 1.75 Å, Crystal structure of Brd4 bromodomain 1 with propionylated histone H3-K(prop)23
4QQ4 1.75 Å, CW-type zinc finger of MORC3 in complex with the amino terminus of histone H3
1PDQ 1.76 Å, Polycomb chromodomain complexed with the histone H3 tail containing trimethyllysine 27.

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