4HGA: Variant histone H3.3-H4 heterodimer

Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX. Determined by X-ray diffraction at 2.8 Å resolution. Released 7 Nov 2012.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,081
Mol. weight: 52.91 kDa
Ligands: PC4
Released: 7 Nov 2012

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

Secondary structure: helices and β-sheets

4HGA 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: 12 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	183-206	24
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	283-285	3
α-helix	286-299	14
α-helix	306-334	29
α-helix	346-348	3
α-helix	350-353	4
α-helix	355-386	32

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	48-58	11
α-helix	64-77	14
β-strand	83-85	3	1
α-helix	86-110	25
β-strand	119	1	2
α-helix	121-131	11

Chain C: 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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Death domain-associated protein 6	A	protein	213	Homo sapiens	Q9UER7 (AlphaFold model)
Histone H3.3	B	protein	136	Homo sapiens	P84243 (AlphaFold model)
Histone H4	C	protein	103	Homo sapiens	P62805 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4HGA_1 Death domain-associated protein 6 (chains A)
GPLQDPSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSAYLQEARLKRKLIRLFG
RLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGPDTFPDYGDVLRAVEKAA
ARHSLGLPRQQLQLMAQDAFRDVGIRLQERRHLDLIYNFGCHLTDDYRPGVDPALSDPVL
ARRLRENRSLAMSRLDEVISKYAMLQDKSEEGE

Sequence of entity 2 (B), FASTA

>4HGA_2 Histone H3.3 (chains B)
MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 3 (C), FASTA

>4HGA_3 Histone H4 (chains C)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Ligands and cofactors

ID	Name	Formula	Copies
PC4	Tetrachloroplatinate(ii)	Cl4 Pt	4

Primary citation

Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX. Liu, C.P., Xiong, C.Y., Wang, M.Z. et al. Nat Struct Mol Biol (2012) 19:1287-1292. DOI 10.1038/nsmb.2439 · PubMed

Other PDB entries of the same protein (UniProt Q9UER7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GRQ 1.58 Å, Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide
4H9N 1.95 Å, Complex structure 1 of DAXX/H3.3(sub5)/H4
4H9Q 1.95 Å, Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4
4H9O 2.05 Å, Complex structure 2 of DAXX/H3.3(sub5,G90M)/H4
4H9R 2.2 Å, Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4
4H9P 2.2 Å, Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4
5Y18 2.2 Å, Crystal structure of DAXX helical bundle domain in complex with ATRX
4H9S 2.6 Å, Complex structure 6 of DAXX/H3.3(sub7)/H4
5Y6O 3.1 Å, Crystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX
5KDM 3.5 Å, Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX…
2KQS Phosphorylation of SUMO-interacting motif by CK2 enhances Daxx SUMO binding activity
2KZS DAXX helical bundle (DHB) domain

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