3RWR: Human XRCC4-XLF complex

Crystal structure of the human XRCC4-XLF complex. Determined by X-ray diffraction at 3.94 Å resolution. Released 7 Dec 2011.

Method: X-ray diffraction
Resolution: 3.94 Å
Organism: Homo sapiens
Chains: 24
Atoms: 36,833
Mol. weight: 558.22 kDa
Ligands: TBR
Released: 7 Dec 2011

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

Secondary structure: helices and β-sheets

3RWR contains 189 α-helices and 265 β-strands across 24 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: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	6-7	2	2
β-strand	19-20	2	2
β-strand	23	1	1
β-strand	33-35	3	3
β-strand	36-37	2	2
β-strand	44-46	3	3
α-helix	49-51	3
α-helix	53-56	4
α-helix	63-65	3
β-strand	85-89	5	4
β-strand	94-99	6	4
β-strand	106-109	4	4
β-strand	114	1	3
α-helix	119-141	23
α-helix	144-146	3

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	502	1	5
β-strand	510	1	6
β-strand	519-525	7	5
β-strand	527-537	11	5
β-strand	542-548	7	5
α-helix	563-570	8
β-strand	585-589	5	6
β-strand	594-598	5	6
β-strand	606	1	7
β-strand	607	1	6
β-strand	614-615	2	5
α-helix	619-631	13
α-helix	632-636	5
α-helix	638-645	8
α-helix	651-654	4

Chain D: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
β-strand	15-17	3	8
β-strand	22-25	4	8
β-strand	28	1	8
β-strand	35-39	5	8
β-strand	44-48	5	8
α-helix	51-61	11
α-helix	69-76	8
β-strand	95-98	4	8
β-strand	103-108	6	8
α-helix	112-114	3
β-strand	120-125	6	8
α-helix	128-131	4
α-helix	136-169	34
α-helix	186-192	7
α-helix	193-197	5
α-helix	198-200	3
α-helix	208-212	5
α-helix	215-224	10

Chain E: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	502-509	8
β-strand	525-529	5	9
β-strand	534-539	6	9
β-strand	544-547	4	9
α-helix	551-561	11
α-helix	569-585	17
β-strand	593-600	8	9
β-strand	603-610	8	9
β-strand	611-612	2	10
β-strand	615-616	2	10
β-strand	619	1	9
β-strand	623-625	3	9
α-helix	626-627	2
α-helix	628-633	6
α-helix	636-665	30
α-helix	666-670	5
α-helix	686-693	8
α-helix	699-702	4
α-helix	715-725	11

Chain F: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	11
β-strand	20-23	4	11
α-helix	28-30	3
β-strand	33-36	4	11
β-strand	43-44	2	11
α-helix	49-57	9
α-helix	63-71	9
β-strand	84-89	6	12
β-strand	94-99	6	12
β-strand	109-112	4	12
α-helix	114	1
β-strand	115	1	11
α-helix	116	1
α-helix	119-136	18
α-helix	138-150	13

Chain G: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	505-508	4	13
β-strand	518-523	6	13
β-strand	532-535	4	13
β-strand	536	1	14
β-strand	543	1	14
β-strand	546-547	2	13
α-helix	549-553	5
α-helix	555-558	4
α-helix	563-573	11
β-strand	583-589	7	15
β-strand	594-600	7	15
β-strand	601	1	16
β-strand	604	1	16
β-strand	607-611	5	15
β-strand	615	1	14
α-helix	619-645	27
α-helix	650-652	3

Chain H: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	17	1	17
β-strand	18	1	18
β-strand	22	1	17
β-strand	24-26	3	19
β-strand	29-30	2	19
β-strand	33-39	7	19
β-strand	44-50	7	19
α-helix	51-59	9
β-strand	65	1	7
α-helix	69-79	11
β-strand	95	1	18
β-strand	98-100	3	19
β-strand	103-105	3	19
β-strand	110-112	3	20
β-strand	115-117	3	20
β-strand	122-125	4	19
α-helix	126-127	2
α-helix	128-131	4
α-helix	132-136	5
α-helix	137-168	32
α-helix	186-192	7
α-helix	193-195	3
α-helix	198-201	4
α-helix	208-212	5
α-helix	215-225	11

Chain I: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	503-510	8
α-helix	512-513	2
β-strand	514-517	4	21
β-strand	522-525	4	21
β-strand	538-539	2	21
β-strand	544-546	3	21
α-helix	551-561	11
α-helix	569-584	16
β-strand	598-600	3	21
β-strand	603-612	10	21
β-strand	615-625	11	21
α-helix	628-630	3
α-helix	631-636	6
α-helix	637-666	30
α-helix	667-671	5
α-helix	682-684	3
α-helix	686-692	7
α-helix	693-697	5
α-helix	698-701	4
α-helix	708-712	5
α-helix	715-725	11

16 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA repair protein XRCC4	A, B, F, G, J, K, N, P, R, U, V, Y	protein	163	Homo sapiens	Q13426 (AlphaFold model)
Non-homologous end-joining factor 1	D, E, H, I, L, M, O, Q, S, T, W, X	protein	230	Homo sapiens	Q9H9Q4 (AlphaFold model)

Sequence of entity 1 (A, B, F, G, J, K, N, P, R, U, V, Y), FASTA

>3RWR_1 DNA repair protein XRCC4 (chains A, B, F, G, J, K, N, P, R, U, V, Y)
MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMA
MEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPA
EVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDHHHHHH

Sequence of entity 2 (D, E, H, I, L, M, O, Q, S, T, W, X), FASTA

>3RWR_2 Non-homologous end-joining factor 1 (chains D, E, H, I, L, M, O, Q, S, T, W, X)
MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKE
LNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWN
FHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLK
TEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
TBR	Hexatantalum dodecabromide	Br12 Ta6	8

Primary citation

Structure of human XLF-XRCC4: assembly of a functional DNA repair complex. Andres, N.S., Wyman, C., Modesti, M. et al. To be published.

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

Browse structure collections

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