3QLA: Hexagonal complex structure of ATRX ADD

Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide. Determined by X-ray diffraction at 1.6 Å resolution. Released 15 Jun 2011.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,630
Mol. weight: 33.24 kDa
Ligands: ZN
Released: 15 Jun 2011

Explore 3QLA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QLA contains 16 α-helices and 18 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	170	1	1
β-strand	177	1	1
α-helix	183-185	3
β-strand	186-188	3	2
β-strand	195-197	3	2
α-helix	198-206	9
α-helix	208-210	3
β-strand	211	1	3
β-strand	217	1	3
β-strand	228-231	4	4
β-strand	238-240	3	4
α-helix	241-256	16
α-helix	262-264	3
α-helix	271-273	3
α-helix	274-285	12

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-5	3	4
α-helix	7-9	3

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	170	1	5
β-strand	177	1	5
α-helix	183-185	3
β-strand	187-188	2	6
β-strand	195-196	2	6
α-helix	198-206	9
α-helix	208-210	3
β-strand	211	1	7
β-strand	217	1	7
β-strand	228-231	4	8
β-strand	238-240	3	8
α-helix	241-248	8
α-helix	250-256	7
α-helix	271-273	3
α-helix	274-285	12

Chain F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-5	4	8
α-helix	7-9	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcriptional regulator ATRX	A, D	protein	129	Homo sapiens	P46100 (AlphaFold model)
peptide of Histone H3.3	C, F	protein	15	Homo sapiens	P84243 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>3QLA_1 Transcriptional regulator ATRX (chains A, D)
GPLGSMGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQC
RWCAEGGNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPEPLLDLVTAC
NSVYENLEQ

Sequence of entity 2 (C, F), FASTA

>3QLA_2 peptide of Histone H3.3 (chains C, F)
ARTKQTARKSTGGKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Water and common crystallization additives (K) are not listed.

Primary citation

ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome. Iwase, S., Xiang, B., Ghosh, S. et al. Nat Struct Mol Biol (2011) 18:769-776. DOI 10.1038/nsmb.2062 · PubMed

Other PDB entries of the same protein (UniProt P46100 (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
6G0O 1.4 Å, Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated…
5GRQ 1.58 Å, Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide
3QLN 1.9 Å, Crystal structure of ATRX ADD domain in free state
5Y18 2.2 Å, Crystal structure of DAXX helical bundle domain in complex with ATRX
3QLC 2.5 Å, Complex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide
4W5A 2.6 Å, Complex structure of ATRX ADD bound to H3K9me3S10ph peptide
5Y6O 3.1 Å, Crystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX
9L06 3.4 Å, The cryo-EM structure of ATRX in complex with the nucleosome in the ADP.BeFx-bound state…
2JM1 Structures and chemical shift assignments for the ADD domain of the ATRX protein
2LBM Solution structure of the ADD domain of ATRX complexed with histone tail H3 1-15 K9me3
2LD1 Structures and chemical shift assignments for the ADD domain of the ATRX protein

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