3II6: Human Xrcc4

Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV. Determined by X-ray diffraction at 2.4 Å resolution. Released 11 Aug 2009.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,925
Mol. weight: 154.21 kDa
Released: 11 Aug 2009

Explore 3II6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3II6 contains 40 α-helices and 65 β-strands across 6 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
β-strand	13-23	11	1
β-strand	31-37	7	1
β-strand	42-44	3	1
β-strand	46-48	3	1
α-helix	49-58	10
α-helix	63-74	12
β-strand	84-88	5	2
β-strand	94-100	7	2
β-strand	105-112	8	2
β-strand	114-115	2	1
α-helix	119-200	82

Chain B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	3
β-strand	18-25	8	3
β-strand	27-37	11	3
β-strand	42-43	2	3
β-strand	46	1	3
α-helix	55-58	4
α-helix	64-74	11
β-strand	86-88	3	4
β-strand	94-97	4	4
β-strand	109-112	4	4
α-helix	119-200	82

Chain C: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	5
β-strand	13-23	11	5
β-strand	25	1	6
β-strand	27	1	6
β-strand	31-37	7	5
β-strand	42-44	3	5
β-strand	46-48	3	5
α-helix	49-58	10
α-helix	65-74	10
β-strand	84-89	6	7
β-strand	94-101	8	7
β-strand	104-112	9	7
β-strand	114-115	2	5
α-helix	119-199	81

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	8
β-strand	18-25	8	8
β-strand	27-37	11	8
β-strand	42-46	5	8
α-helix	55-58	4
α-helix	63-74	12
β-strand	86-88	3	9
β-strand	94-97	4	9
β-strand	109-112	4	9
α-helix	121-199	79

Chain X: 13 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	663-666	4	10
α-helix	675-684	10
β-strand	688-689	2	10
β-strand	697-701	5	10
α-helix	707-714	8
β-strand	720-721	2	10
α-helix	723-732	10
α-helix	740-742	3
β-strand	743-745	3	10
α-helix	748-753	6
β-strand	758	1	11
β-strand	764	1	11
α-helix	771-779	9
α-helix	789-803	15
α-helix	809-811	3
β-strand	817-820	4	12
β-strand	823	1	13
α-helix	829-831	3
β-strand	832	1	13
α-helix	837-847	11
β-strand	851-853	3	12
β-strand	858	1	14
β-strand	860	1	14
β-strand	862-865	4	12
α-helix	872-880	9
β-strand	887-890	4	12
α-helix	892-899	8
α-helix	906-908	3
β-strand	910	1	12

Chain Y: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	663-666	4	15
α-helix	675-684	10
β-strand	688-689	2	15
β-strand	697-701	5	15
α-helix	707-712	6
β-strand	720-721	2	15
α-helix	723-732	10
α-helix	736-738	3
α-helix	740-742	3
β-strand	743-745	3	15
α-helix	748-757	10
β-strand	758	1	16
β-strand	764	1	16
α-helix	771-780	10
α-helix	782-783	2
α-helix	789-802	14
α-helix	805-807	3
α-helix	809-811	3
β-strand	817-820	4	17
β-strand	823	1	18
β-strand	832	1	18
α-helix	837-847	11
β-strand	851-853	3	17
β-strand	862-865	4	17
α-helix	872-881	10
β-strand	887-890	4	17
α-helix	892-899	8
α-helix	906-908	3
β-strand	910	1	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA repair protein XRCC4	A, B, C, D	protein	203	Homo sapiens	Q13426 (AlphaFold model)
DNA ligase 4	X, Y	protein	263	Homo sapiens	P49917 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3II6_1 DNA repair protein XRCC4 (chains A, B, C, D)
MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDME
MEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPA
EVIRELICYCLDTTAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRF
ILVLNEKKTKIRSLHNKLLNAAQ

Sequence of entity 2 (X, Y), FASTA

>3II6_2 DNA ligase 4 (chains X, Y)
GAMGSKISNIFEDVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGPDTYCVIAGSENIR
VKNIILSNKHDVVKPAWLLECFKTKSFVPWQPRFMIHMCPSTKEHFAREYDCYGDSYFID
TDLNQLKEVFSGIKNSNEQTPEEMASLIADLEYRYSWDCSPLSMFRRHTVYLDSYAVIND
LSTKNEGTRLAIKALELRFHGAKVVSCLAEGVSHVIIGEDHSRVADFKAFRRTFKRKFKI
LKESWVTDSIDKCELQEENQYLI

Primary citation

Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4. Wu, P.Y., Frit, P., Meesala, S. et al. Mol Cell Biol (2009) 11:3163-3172. 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
1IK9 2.3 Å, Crystal structure of a XRCC4-DNA ligase IV complex
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
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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