4HTP: DBD domain of human DNA ligase IV

Crystal structure of the DBD domain of human DNA ligase IV bound to Artemis peptide. Determined by X-ray diffraction at 2.25 Å resolution. Released 26 Dec 2012.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,872
Mol. weight: 57.6 kDa
Released: 26 Dec 2012

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

Secondary structure: helices and β-sheets

4HTP contains 31 α-helices and 4 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: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
β-strand	15	1	1
α-helix	16-28	13
α-helix	32-53	22
α-helix	65-71	7
α-helix	73-75	3
α-helix	86-96	11
α-helix	104-110	7
α-helix	125-133	9
β-strand	144	1	1
α-helix	145-160	16
α-helix	164-176	13
α-helix	180-191	12
α-helix	200-207	8
α-helix	211-218	8
α-helix	221-227	7

Chain B: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	15	1	2
α-helix	16-28	13
α-helix	32-54	23
α-helix	65-71	7
α-helix	73-75	3
α-helix	86-96	11
α-helix	104-110	7
α-helix	125-136	12
β-strand	144	1	2
α-helix	145-160	16
α-helix	164-176	13
α-helix	180-191	12
α-helix	200-207	8
α-helix	211-218	8
α-helix	221-227	7
α-helix	234-236	3

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	486-488	3
α-helix	489-491	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA ligase 4	A, B	protein	240	Homo sapiens	P49917 (AlphaFold model)
Protein artemis	C, E	protein	11	Homo sapiens	Q96SD1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4HTP_1 DNA ligase 4 (chains A, B)
MAASQTSQTVASHVPFADLCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKNHKDV
TDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPTGTHG
DAGDFAMIAYFVLKPRCLQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLITQSSA
LEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVCRQLHDPSVGLSDISI

Sequence of entity 2 (C, E), FASTA

>4HTP_2 Protein artemis (chains C, E)
DVPQWEVFFKR

Primary citation

Structural Basis of DNA Ligase IV-Artemis Interaction in Nonhomologous End-Joining. De Ioannes, P., Malu, S., Cortes, P. et al. Cell Rep (2012) 2:1505-1512. DOI 10.1016/j.celrep.2012.11.004 · PubMed

Other PDB entries of the same protein (UniProt P49917 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1IK9 2.3 Å, Crystal structure of a XRCC4-DNA ligase IV complex
3II6 2.4 Å, Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV.
3W1B 2.4 Å, Crystal Structure of Human DNA ligase IV-Artemis Complex (Mercury Derivative)
6BKG 2.4 Å, Human LigIV catalytic domain with bound DNA-adenylate intermediate in closed conformation
3W1G 2.55 Å, Crystal Structure of Human DNA ligase IV-Artemis Complex (Native)
7D9Y 2.76 Å, DNA binding domain of human DNA Ligase IV mutant - A3V
9CQ3 2.8 Å, The gap-filling complex with Pol mu engaged in the NHEJ pathway
9N81 2.8 Å, A gap-filling complex with Pol mu engaged in the NHEJ Pathway
4HTO 2.81 Å, Crystal structure of the DBD domain of human DNA ligase IV Apo form
3W5O 2.84 Å, Crystal Structure of Human DNA ligase IV
7D9K 2.9 Å, DNA binding domain of human DNA Ligase IV - Wild type
3VNN 2.9 Å, Crystal Structure of a sub-domain of the nucleotidyltransferase (adenylation) domain of…

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