1IK9: XRCC4-DNA ligase IV complex

Crystal structure of a XRCC4-DNA ligase IV complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 21 Nov 2001.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,736
Mol. weight: 53.26 kDa
Released: 21 Nov 2001

Explore 1IK9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1IK9 contains 9 α-helices and 19 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: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	1
β-strand	13-25	13	1
β-strand	27-37	11	1
β-strand	42-48	7	1
α-helix	49-58	10
α-helix	63-74	12
β-strand	84-89	6	1
β-strand	94-100	7	1
β-strand	105-112	8	1
β-strand	114-115	2	1
α-helix	119-210	92

Chain B: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	2
β-strand	10	1	3
β-strand	18-24	7	2
α-helix	28-30	3
β-strand	31-37	7	2
β-strand	42-48	7	2
α-helix	49-59	11
α-helix	63-74	12
β-strand	84-88	5	3
β-strand	94-101	8	3
β-strand	104-112	9	3
β-strand	114-115	2	2
α-helix	119-169	51
α-helix	172-200	29

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	758	1	4
β-strand	764	1	4
α-helix	771-779	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA repair protein XRCC4	A, B	protein	213	Homo sapiens	Q13426 (AlphaFold model)
DNA ligase IV	C	protein	37	Homo sapiens	P49917 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1IK9_1 DNA REPAIR PROTEIN XRCC4 (chains A, B)
MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMA
MEKGKYVGELRKALLSGAGPADVYTFNFSKESAYFFFEKNLKDVSFRLGSFNLEKVENPA
EVIRELIAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETDLYKRF
ILVLNEKKTKIRSLHNKLLNAAQEREKDIKQEG

Sequence of entity 2 (C), FASTA

>1IK9_2 DNA LIGASE IV (chains C)
PSTKEHFAREYDCYGDSYFIDTDLNQLKEVFSGIKNS

Primary citation

Crystal structure of an Xrcc4-DNA ligase IV complex. Sibanda, B.L., Critchlow, S.E., Begun, J. et al. Nat Struct Biol (2001) 8:1015-1019. DOI 10.1038/nsb725 · PubMed

Other PDB entries of the same protein (UniProt Q13426 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5E50 1.38 Å, APLF/XRCC4 complex
7M3P 2.0 Å, Xrcc4-Spc110p(164-207) fusion
3MUD 2.2 Å, Structure of the Tropomyosin Overlap Complex from Chicken Smooth Muscle
5CHX 2.3 Å, Crystal Structure of amino acids 1590-1657 of MYH7
5CJ0 2.3 Å, Crystal Structure of Amino Acids 1631-1692 of MYH7
4XA4 2.33 Å, Crystal Structure of the coiled-coil surrounding Skip 3 of MYH7
3II6 2.4 Å, Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV.
5WJ7 2.5 Å, Crystal Structure of Amino Acids 1733-1797 of Human Beta Cardiac Myosin Fused to Xrcc4
6ABO 2.65 Å, human XRCC4 and IFFO1 complex
1FU1 2.7 Å, Crystal structure of human XRCC4
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

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