3SR2: Human XLF-XRCC4 Complex

Crystal Structure of Human XLF-XRCC4 Complex. Determined by X-ray diffraction at 3.97 Å resolution. Released 20 Jul 2011.

Method: X-ray diffraction
Resolution: 3.97 Å
Organism: Homo sapiens
Chains: 8
Atoms: 11,363
Mol. weight: 168.5 kDa
Released: 20 Jul 2011

Explore 3SR2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3SR2 contains 60 α-helices and 71 β-strands across 8 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: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	10	1	2
β-strand	19-24	6	1
α-helix	28-30	3
β-strand	32-37	6	1
β-strand	42-47	6	1
α-helix	50-59	10
α-helix	63-73	11
β-strand	83-88	6	2
β-strand	94-100	7	2
β-strand	107-112	6	2
β-strand	114-115	2	1
α-helix	119-136	18

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	3
β-strand	19-24	6	3
α-helix	28-30	3
β-strand	31-37	7	3
β-strand	42-48	7	3
α-helix	49-58	10
α-helix	63-72	10
β-strand	83-89	7	4
β-strand	93-100	8	4
β-strand	107-112	6	4
β-strand	115	1	3
α-helix	119-135	17

Chain C: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	14-15	2	5
β-strand	18	1	6
β-strand	21	1	6
β-strand	24-30	7	5
β-strand	33-39	7	5
β-strand	44-50	7	5
α-helix	51-58	8
α-helix	69-84	16
β-strand	95-100	6	5
β-strand	103-111	9	5
β-strand	116-125	10	5
α-helix	128-130	3
α-helix	131-136	6
α-helix	137-167	31
α-helix	186-196	11
α-helix	198-201	4
α-helix	208-222	15

Chain D: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
α-helix	12-13	2
β-strand	14-15	2	7
β-strand	24-29	6	7
β-strand	33-39	7	7
β-strand	44-50	7	7
α-helix	51-61	11
α-helix	69-77	9
β-strand	94-100	7	8
β-strand	103-110	8	8
β-strand	117-123	7	8
β-strand	124-125	2	7
α-helix	126-127	2
α-helix	128-130	3
α-helix	131-136	6
α-helix	137-168	32
α-helix	177-179	3
α-helix	180-184	5
α-helix	187-196	10
α-helix	198-201	4
α-helix	208-211	4
α-helix	213-222	10

Chain E: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	9
β-strand	18-24	7	9
α-helix	28-30	3
β-strand	32-37	6	9
β-strand	42-47	6	9
α-helix	49-59	11
α-helix	63-71	9
β-strand	83-87	5	10
β-strand	94-100	7	10
β-strand	105	1	10
β-strand	109-112	4	10
β-strand	115	1	9
α-helix	119-139	21

Chain F: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	11
β-strand	19-24	6	11
β-strand	32-37	6	11
β-strand	42-47	6	11
α-helix	49-59	11
α-helix	63-69	7
β-strand	83-87	5	12
β-strand	95-101	7	12
β-strand	104-105	2	12
β-strand	109-111	3	12
β-strand	114-115	2	11
α-helix	119-137	19

Chain G: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
β-strand	14-15	2	13
β-strand	18	1	14
β-strand	21	1	14
β-strand	24-29	6	13
β-strand	34-39	6	13
β-strand	44-49	6	13
α-helix	52-56	5
β-strand	66	1	12
α-helix	69-80	12
β-strand	94-100	7	15
β-strand	103-110	8	15
β-strand	117-123	7	15
β-strand	124-125	2	13
α-helix	128-130	3
α-helix	131-135	5
α-helix	136-167	32
α-helix	181-183	3
α-helix	186-196	11
α-helix	198-201	4
α-helix	208-213	6
α-helix	215-222	8

Chain H: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
α-helix	4-8	5
β-strand	15	1	16
β-strand	24-29	6	16
β-strand	33-39	7	16
β-strand	44-50	7	16
α-helix	51-61	11
α-helix	69-77	9
β-strand	94-98	5	17
β-strand	105-110	6	17
β-strand	117-122	6	17
β-strand	124-125	2	16
α-helix	126-127	2
α-helix	128-130	3
α-helix	131-136	6
α-helix	137-168	32
α-helix	186-196	11
α-helix	208-211	4
α-helix	215-223	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA repair protein XRCC4	A, B, E, F	protein	145	Homo sapiens	Q13426 (AlphaFold model)
Non-homologous end-joining factor 1	C, D, G, H	protein	229	Homo sapiens	Q9H9Q4 (AlphaFold model)

Sequence of entity 1 (A, B, E, F), FASTA

>3SR2_1 DNA repair protein XRCC4 (chains A, B, E, F)
GPLGSMERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQE
ADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEK
VENPAEVIRELICYCLDTIAENQAK

Sequence of entity 2 (C, D, G, H), FASTA

>3SR2_2 Non-homologous end-joining factor 1 (chains C, D, G, H)
GPLGSMEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVS
QRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGL
PFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLI
RDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQ

Primary citation

XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair. Hammel, M., Rey, M., Yu, Y. et al. J Biol Chem (2011) 286:32638-32650. DOI 10.1074/jbc.M111.272641 · 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
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

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