5E50: APLF/XRCC4 complex

APLF/XRCC4 complex. Determined by X-ray diffraction at 1.38 Å resolution. Released 18 Nov 2015.

Method: X-ray diffraction
Resolution: 1.38 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,285
Mol. weight: 26.66 kDa
Ligands: MG
Released: 18 Nov 2015

Explore 5E50 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E50 contains 7 α-helices and 28 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: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	-3	1	1
β-strand	4-9	6	2
α-helix	13-15	3
β-strand	16-17	2	2
α-helix	18-19	2
β-strand	21-25	5	3
β-strand	28	1	4
β-strand	33	1	4
β-strand	43-48	6	3
β-strand	51-56	6	3
β-strand	58	1	5
β-strand	63-65	3	2
β-strand	73-74	2	2
α-helix	75-76	2
β-strand	81-83	3	3
β-strand	88-92	5	2
β-strand	95-103	9	2

Chain B: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	-3	1	5
β-strand	4-9	6	6
β-strand	16-17	2	6
α-helix	18-19	2
β-strand	21-25	5	7
β-strand	28	1	8
β-strand	33	1	8
β-strand	43-48	6	7
β-strand	51-56	6	7
β-strand	58	1	1
β-strand	63-65	3	6
β-strand	73-74	2	6
α-helix	75-76	2
β-strand	81-83	3	7
β-strand	88-92	5	6
β-strand	95-103	9	6

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	232-234	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aprataxin and PNK-like factor	A, B	protein	111	Homo sapiens	Q8IW19 (AlphaFold model)
XRCC4	C, D	protein	9	Homo sapiens	Q13426 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5E50_1 Aprataxin and PNK-like factor (chains A, B)
GPLGSMSGGFELQPRDGGPRVALAPGETVIGRGPLLGITDKRVSRRHAILEVAGGQLRIK
PIHTNPCFYQSSEKSQLLPLKPNLWCYLNPGDSFSMLVDKYIFRILSIPSA

Sequence of entity 2 (C, D), FASTA

>5E50_2 XRCC4 (chains C, D)
AYDESTDEE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Primary citation

Versatility in phospho-dependent molecular recognition of the XRCC1 and XRCC4 DNA-damage scaffolds by aprataxin-family FHA domains. Cherry, A.L., Nott, T.J., Kelly, G. et al. DNA Repair (Amst) (2015) 35:116-125. DOI 10.1016/j.dnarep.2015.10.002 · PubMed

Other PDB entries of the same protein (UniProt Q8IW19 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5W7W 1.35 Å, Crystal Structure of FHA domain of human APLF
6TYZ 1.51 Å, Structure of Ku80 von Willebrand domain complexed with APLF Ku Binding Motif
6TYW 1.7 Å, Structure of Ku80 von Willebrand domain S229A mutant complexed with APLF Ku Binding Motif
5W7X 2.0 Å, Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide
5W7Y 2.1 Å, Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated…
6YN1 2.35 Å, Crystal structure of histone chaperone APLF acidic domain bound to the histone…
6TYT 2.4 Å, Structure of Ku80 von Willebrand domain S229A mutant complexed with APLF and XLF Ku…
6ERF 3.01 Å, Complex of APLF factor and Ku heterodimer bound to DNA
2KQB First PBZ domain of human APLF protein
2KQC Second PBZ domain of human APLF protein
2KQD First PBZ domain of human APLF protein in complex with ribofuranosyladenosine
2KQE Second PBZ domain of human APLF protein in complex with ribofuranosyladenosine

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