4H9N: Complex structure 1 of DAXX/H3.3(sub5)/H4

Complex structure 1 of DAXX/H3.3(sub5)/H4. Determined by X-ray diffraction at 1.95 Å resolution. Released 10 Oct 2012.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,499
Mol. weight: 52.1 kDa
Ligands: PO4
Released: 10 Oct 2012

Explore 4H9N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4H9N contains 19 α-helices and 5 β-strands across 3 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	48-58	11
α-helix	64-78	15
β-strand	83-85	3	1
α-helix	86-109	24
β-strand	119	1	2
α-helix	121-131	11

Chain B: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	46	1	2
α-helix	48-75	28
β-strand	80-81	2	1
α-helix	83-90	8

Chain C: 12 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	185-206	22
β-strand	209-210	2	1
α-helix	214-216	3
α-helix	221-242	22
α-helix	252-254	3
α-helix	256-258	3
α-helix	265-275	11
α-helix	286-299	14
α-helix	306-333	28
α-helix	339-341	3
α-helix	346-348	3
α-helix	350-353	4
α-helix	355-384	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.3	A	protein	135	Homo sapiens	P84243 (AlphaFold model)
Histone H4	B	protein	102	Homo sapiens	P62805 (AlphaFold model)
Death domain-associated protein 6	C	protein	212	Homo sapiens	Q9UER7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4H9N_1 Histone H3.3 (chains A)
ARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEAAEAFLVALFEDTNLCTIHAKRVTIF
PKDIQLARRIRGERA

Sequence of entity 2 (B), FASTA

>4H9N_2 Histone H4 (chains B)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C), FASTA

>4H9N_3 Death domain-associated protein 6 (chains C)
SPRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSAYLQEARLKRKLIRLFG
RLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGPDTFPDYGDVLRAVEKAA
ARHSLGLPRQQLQLMAQDAFRDVGIRLQERRHLDLIYNFGCHLTDDYRPGVDPALSDPVL
ARRLRENRSLAMSRLDEVISKYAMLQDKSEEG

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	9

Primary citation

DAXX chaperone envelops an H3.3/H4 dimer dictating H3.3-specific read out. Elsasser, S.J., Huang, H., Lewis, P.W. et al. To be published.

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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