5GRQ: DHB domain of Daxx

Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide. Determined by X-ray diffraction at 1.58 Å resolution. Released 27 Sept 2017.

Method: X-ray diffraction
Resolution: 1.58 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,331
Mol. weight: 29.16 kDa
Ligands: ZN
Released: 27 Sept 2017

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

Secondary structure: helices and β-sheets

5GRQ contains 17 α-helices and 4 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.

Chains A and B: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	56-58	3
α-helix	60-77	18
α-helix	84-93	10
β-strand	95	1	1
α-helix	97-100	4
α-helix	103-118	16
α-helix	120-122	3
α-helix	123-136	14
β-strand	138	1	1

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1267-1282	16

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1263-1265	3
α-helix	1267-1282	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Death domain-associated protein 6	A, B	protein	90	Homo sapiens	Q9UER7 (AlphaFold model)
Transcriptional regulator ATRX	C, D	protein	30	Homo sapiens	P46100 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5GRQ_1 Death domain-associated protein 6 (chains A, B)
GKKCYKLENEKLFEEFLELCKMQTADHPEVVPFLYNRQQRAHSLFLASAEFCNILSRVLS
RARSRPAKLYVYINELCTVLKAHSAKKKLN

Sequence of entity 2 (C, D), FASTA

>5GRQ_2 Transcriptional regulator ATRX (chains C, D)
VTVDDDDDDNDPENRIAKKMLLEEIKANLS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	11

Water and common crystallization additives (CL, GOL, ACT) are not listed.

Primary citation

Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide. Li, H. To be published.

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

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
4HGA 2.8 Å, Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX
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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