8EZA: NHEJ Long-range complex with PAXX

NHEJ Long-range complex with PAXX. Determined by electron microscopy at 4.39 Å resolution. Released 14 Jun 2023.

Method: Electron microscopy
Resolution: 4.39 Å
Organism: Homo sapiens
Chains: 22
Atoms: 93,588
Mol. weight: 1758.48 kDa
Ligands: ATP
Released: 14 Jun 2023

Explore 8EZA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EZA contains 678 α-helices and 238 β-strands across 18 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.

Chains A and J: 19 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	34	1
β-strand	35-43	9	14
α-helix	46-49	4
α-helix	59-77	19
β-strand	82-88	7	14
β-strand	94	1	14
β-strand	102-109	8	14
β-strand	112	1	15
α-helix	113-120	8
α-helix	124-130	7
α-helix	143-156	14
β-strand	161-169	9	14
α-helix	180-195	16
β-strand	199-203	5	14
α-helix	239-243	5
β-strand	257-262	6	16
β-strand	268-274	7	16
β-strand	277	1	17
α-helix	282-285	4
β-strand	286-289	4	18
β-strand	295	1	18
β-strand	297-298	2	19
β-strand	303-304	2	20
β-strand	310	1	20
α-helix	313-315	3
β-strand	316	1	21
β-strand	318-322	5	22
β-strand	325-329	5	22
α-helix	333-335	3
β-strand	344-352	9	16
β-strand	366-370	5	16
α-helix	378-392	15
β-strand	394-401	8	16
α-helix	407-408	2
β-strand	409-415	7	16
β-strand	432-436	5	16
α-helix	440-442	3
β-strand	443	1	23
β-strand	445	1	24
α-helix	456-468	13
β-strand	470	1	25
α-helix	475-477	3
α-helix	481-495	15
α-helix	511-518	8
α-helix	522-528	7

Chains B and K: 26 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	44
α-helix	19-21	3
α-helix	30-47	18
β-strand	53-59	7	44
β-strand	65	1	44
β-strand	77-84	8	44
α-helix	88-92	5
α-helix	93-97	5
α-helix	107-124	18
β-strand	130-135	6	44
α-helix	147-156	10
β-strand	160-165	6	44
α-helix	199-216	18
α-helix	217-223	7
β-strand	224-226	3	44
α-helix	227-231	5
β-strand	243	1	24
α-helix	244-246	3
β-strand	247-251	5	25
β-strand	259-268	10	25
β-strand	277	1	22
β-strand	280	1	21
β-strand	289-290	2	20
β-strand	295-296	2	19
β-strand	297	1	45
β-strand	302	1	45
α-helix	306-309	4
β-strand	310-316	7	18
β-strand	317	1	15
β-strand	319-322	4	18
α-helix	325-331	7
β-strand	340-347	8	25
α-helix	348-350	3
β-strand	360-366	7	25
α-helix	367	1
α-helix	371-382	12
β-strand	389-395	7	25
α-helix	402-403	2
β-strand	404-413	10	25
β-strand	416-423	8	25
β-strand	430	1	17
α-helix	435-437	3
α-helix	441-443	3
α-helix	448-460	13
β-strand	462	1	16
α-helix	479-481	3
α-helix	483-484	2
α-helix	485-499	15
α-helix	504-509	6
α-helix	510-516	7
α-helix	520-536	17
α-helix	548-551	4

Chain C: 253 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
α-helix	24-44	21
α-helix	48-58	11
α-helix	64-71	8
α-helix	79-96	18
α-helix	97-103	7
α-helix	104-117	14
α-helix	121-137	17
α-helix	142-144	3
α-helix	149-158	10
α-helix	159-165	7
α-helix	168-184	17
α-helix	186-189	4
α-helix	193-209	17
α-helix	217-230	14
α-helix	242-256	15
α-helix	266-278	13
α-helix	279-282	4
α-helix	285-288	4
α-helix	290-301	12
α-helix	306-328	23
α-helix	332-334	3
α-helix	335-349	15
α-helix	356-368	13
α-helix	370-373	4
α-helix	378-395	18
α-helix	409-423	15
α-helix	429-431	3
α-helix	432-443	12
α-helix	446-448	3
α-helix	451-469	19
α-helix	473-491	19
α-helix	524-526	3
α-helix	528-536	9
α-helix	538-540	3
α-helix	558-578	21
α-helix	617-633	17
α-helix	643-645	3
α-helix	646-659	14
α-helix	664-679	16
α-helix	700-717	18
α-helix	718-720	3
α-helix	723-734	12
α-helix	738-741	4
α-helix	745-747	3
α-helix	749-759	11
α-helix	763-779	17
α-helix	782-792	11
α-helix	793-796	4
α-helix	797-801	5
α-helix	817-824	8
α-helix	828-837	10
α-helix	845-847	3
α-helix	848-861	14
α-helix	864-867	4
α-helix	868-870	3
α-helix	877-880	4
β-strand	884	1	46
β-strand	893-895	3	47
β-strand	904-906	3	47
α-helix	907-909	3
α-helix	911-920	10
α-helix	924-946	23
α-helix	956	1
α-helix	959-973	15
α-helix	978-994	17
α-helix	1000-1002	3
α-helix	1004-1016	13
α-helix	1023-1042	20
α-helix	1046-1049	4
α-helix	1056-1068	13
α-helix	1072-1089	18
α-helix	1097-1110	14
α-helix	1124-1127	4
α-helix	1128-1130	3
α-helix	1131-1141	11
α-helix	1142-1146	5
α-helix	1164-1174	11
α-helix	1181-1194	14
α-helix	1204-1214	11
α-helix	1217-1224	8
α-helix	1238-1242	5
α-helix	1253-1265	13
α-helix	1267-1270	4
α-helix	1278-1281	4
α-helix	1288	1
α-helix	1289-1293	5
α-helix	1294-1300	7
α-helix	1324	1
α-helix	1325-1330	6
α-helix	1331-1344	14
α-helix	1345-1350	6
α-helix	1356-1359	4
α-helix	1367-1377	11
α-helix	1379-1381	3
α-helix	1384-1386	3
α-helix	1389-1407	19
α-helix	1413-1416	4
α-helix	1428-1431	4
α-helix	1432-1434	3
α-helix	1446-1461	16
α-helix	1464-1467	4
α-helix	1477-1482	6
α-helix	1483-1488	6
α-helix	1499-1504	6
α-helix	1505-1519	15
α-helix	1525-1532	8
β-strand	1537-1538	2	48
β-strand	1553-1554	2	48
α-helix	1555-1562	8
α-helix	1564-1572	9
α-helix	1575-1580	6
α-helix	1581-1585	5
α-helix	1590-1607	18
α-helix	1614-1624	11
α-helix	1626-1629	4
α-helix	1639-1656	18
α-helix	1668-1678	11
α-helix	1686-1699	14
α-helix	1707-1721	15
α-helix	1726-1728	3
β-strand	1731	1	49
β-strand	1733	1	49
α-helix	1734-1751	18
α-helix	1756-1766	11
β-strand	1767	1	50
β-strand	1769	1	50
α-helix	1775-1787	13
α-helix	1791-1806	16
α-helix	1813-1819	7
α-helix	1820-1824	5
α-helix	1825-1828	4
α-helix	1836-1851	16
α-helix	1855-1857	3
α-helix	1861-1863	3
α-helix	1864-1875	12
α-helix	1878-1881	4
α-helix	1886-1889	4
β-strand	1893	1	51
β-strand	1907	1	51
α-helix	1911-1915	5
α-helix	1917-1924	8
α-helix	1934-1955	22
α-helix	1959-1963	5
α-helix	1974-1976	3
α-helix	2094-2105	12
α-helix	2121-2132	12
α-helix	2140-2151	12
α-helix	2154-2157	4
α-helix	2158-2160	3
α-helix	2161-2173	13
α-helix	2184-2200	17
α-helix	2206-2221	16
α-helix	2228-2243	16
α-helix	2253-2261	9
α-helix	2271-2282	12
α-helix	2296-2305	10
α-helix	2306-2308	3
α-helix	2313-2332	20
α-helix	2338-2353	16
α-helix	2357-2368	12
α-helix	2375-2385	11
α-helix	2392-2402	11
α-helix	2411-2417	7
α-helix	2420-2423	4
α-helix	2429-2442	14
α-helix	2443-2445	3
α-helix	2448-2458	11
α-helix	2459-2463	5
α-helix	2467-2484	18
α-helix	2493-2508	16
α-helix	2509-2511	3
α-helix	2515-2526	12
α-helix	2535-2542	8
α-helix	2548-2550	3
α-helix	2551-2563	13
α-helix	2564-2568	5
β-strand	2575	1	52
β-strand	2586-2587	2	53
α-helix	2725-2728	4
α-helix	2736-2767	32
β-strand	2777-2778	2	53
β-strand	2786	1	52
α-helix	2788-2798	11
α-helix	2802-2819	18
α-helix	2820-2822	3
α-helix	2826-2846	21
α-helix	2852-2863	12
α-helix	2868-2870	3
α-helix	2873-2882	10
α-helix	2886-2899	14
α-helix	2920-2932	13
α-helix	2936-2943	8
α-helix	2952-2961	10
α-helix	2965-2977	13
α-helix	2985-2987	3
α-helix	2988-3004	17
α-helix	3008-3017	10
α-helix	3027-3032	6
α-helix	3034-3053	20
α-helix	3060-3068	9
α-helix	3072-3081	10
α-helix	3083-3092	10
α-helix	3096-3116	21
α-helix	3122-3146	25
α-helix	3148-3151	4
α-helix	3155-3165	11
α-helix	3176-3196	21
α-helix	3228-3248	21
α-helix	3252-3266	15
α-helix	3270-3288	19
α-helix	3295-3300	6
α-helix	3304-3307	4
α-helix	3311-3313	3
α-helix	3320-3343	24
α-helix	3348-3351	4
α-helix	3357-3363	7
α-helix	3372-3392	21
α-helix	3409-3427	19
α-helix	3433-3439	7
α-helix	3442-3452	11
α-helix	3453-3455	3
α-helix	3459-3464	6
α-helix	3465-3467	3
α-helix	3468-3474	7
α-helix	3477-3479	3
α-helix	3480-3483	4
α-helix	3487-3489	3
α-helix	3492-3496	5
α-helix	3499-3504	6
α-helix	3511-3524	14
α-helix	3526-3537	12
α-helix	3546-3560	15
α-helix	3567-3577	11
α-helix	3584-3596	13
α-helix	3600-3602	3
α-helix	3603-3613	11
α-helix	3614-3618	5
α-helix	3627-3635	9
α-helix	3638-3642	5
α-helix	3646-3652	7
α-helix	3660-3671	12
α-helix	3676-3678	3
α-helix	3685-3689	5
β-strand	3700	1	54
α-helix	3701	1
α-helix	3713-3715	3
β-strand	3718	1	54
β-strand	3719-3722	4	55
β-strand	3728	1	55
β-strand	3736-3742	7	55
β-strand	3746-3754	9	55
α-helix	3759-3775	17
α-helix	3779-3782	4
β-strand	3797	1	55
β-strand	3800-3804	5	55
α-helix	3805	1
β-strand	3810-3811	2	56
α-helix	3812-3819	8
α-helix	3822-3829	8
α-helix	3839-3842	4
α-helix	3855-3861	7
α-helix	3864-3875	12
α-helix	3879	1
α-helix	3882-3890	9
β-strand	3891	1	46
α-helix	3894-3917	24
β-strand	3928-3931	4	56
β-strand	3936-3939	4	56
α-helix	3948-3951	4
α-helix	3965-3970	6
α-helix	3979-3992	14
α-helix	3995-4001	7
α-helix	4002-4004	3
α-helix	4039-4051	13
β-strand	4054	1	57
α-helix	4056-4065	10
α-helix	4068-4070	3
α-helix	4074-4081	8
β-strand	4096	1	57
α-helix	4100-4112	13
α-helix	4114-4117	4

Chain F: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	58
β-strand	10	1	59
α-helix	16-17	2
β-strand	18-24	7	58
α-helix	28-30	3
β-strand	31-37	7	58
β-strand	42-48	7	58
α-helix	49-59	11
α-helix	65-74	10
β-strand	84-88	5	59
β-strand	94-101	8	59
β-strand	104-112	9	59
β-strand	114-115	2	58
α-helix	119-200	82

Chains G and P: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	62
β-strand	13-24	12	62
β-strand	31-37	7	62
β-strand	42	1	63
β-strand	43-48	6	62
α-helix	49-58	10
α-helix	63-73	11
β-strand	84-88	5	64
β-strand	94-100	7	64
β-strand	105-112	8	64
β-strand	116	1	63
α-helix	119-200	82

Chain H: 16 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-10	9
α-helix	11-13	3
β-strand	14-18	5	40
β-strand	21-29	9	40
β-strand	33-39	7	40
β-strand	44-50	7	40
α-helix	51-61	11
α-helix	69-83	15
β-strand	94-100	7	41
β-strand	103-112	10	41
β-strand	115-123	9	41
β-strand	124-125	2	40
α-helix	126-127	2
α-helix	128-131	4
α-helix	132-136	5
α-helix	137-165	29
α-helix	166-170	5
α-helix	180-184	5
α-helix	186-192	7
α-helix	193-197	5
α-helix	198-201	4
α-helix	208-213	6
α-helix	215-223	9
α-helix	296-298	3

Chain I: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-10	9
α-helix	12-13	2
β-strand	14-17	4	42
β-strand	22-30	9	42
β-strand	33-39	7	42
β-strand	44-50	7	42
α-helix	51-61	11
α-helix	69-78	10
β-strand	94-100	7	43
β-strand	103-112	10	43
β-strand	115-123	9	43
β-strand	124-125	2	42
α-helix	126-127	2
α-helix	128-131	4
α-helix	132-136	5
α-helix	137-168	32
α-helix	182-184	3
α-helix	186-196	11
α-helix	198-202	5
α-helix	208-213	6
α-helix	215-223	9
α-helix	296-298	3

Chain L: 253 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
α-helix	24-44	21
α-helix	48-58	11
α-helix	64-71	8
α-helix	79-96	18
α-helix	97-103	7
α-helix	104-117	14
α-helix	121-137	17
α-helix	142-144	3
α-helix	149-158	10
α-helix	159-165	7
α-helix	168-184	17
α-helix	186-189	4
α-helix	193-209	17
α-helix	217-230	14
α-helix	242-256	15
α-helix	266-278	13
α-helix	279-282	4
α-helix	285-288	4
α-helix	290-301	12
α-helix	306-328	23
α-helix	332-334	3
α-helix	335-349	15
α-helix	356-368	13
α-helix	370-373	4
α-helix	378-395	18
α-helix	409-423	15
α-helix	429-431	3
α-helix	432-443	12
α-helix	446-448	3
α-helix	451-469	19
α-helix	473-491	19
α-helix	524-526	3
α-helix	528-536	9
α-helix	538-540	3
α-helix	558-578	21
α-helix	617-633	17
α-helix	643-645	3
α-helix	646-659	14
α-helix	664-679	16
α-helix	700-717	18
α-helix	718-720	3
α-helix	723-734	12
α-helix	738-741	4
α-helix	745-747	3
α-helix	749-759	11
α-helix	763-779	17
α-helix	782-792	11
α-helix	793-796	4
α-helix	797-801	5
α-helix	817-824	8
α-helix	828-837	10
α-helix	845-847	3
α-helix	848-861	14
α-helix	864-867	4
α-helix	868-870	3
α-helix	877-880	4
β-strand	884	1	28
β-strand	893-895	3	29
β-strand	904-906	3	29
α-helix	907-909	3
α-helix	911-920	10
α-helix	924-946	23
α-helix	956	1
α-helix	959-973	15
α-helix	978-994	17
α-helix	1000-1002	3
α-helix	1004-1016	13
α-helix	1023-1042	20
α-helix	1046-1049	4
α-helix	1056-1068	13
α-helix	1072-1089	18
α-helix	1097-1110	14
α-helix	1124-1127	4
α-helix	1128-1130	3
α-helix	1131-1141	11
α-helix	1142-1144	3
α-helix	1164-1174	11
α-helix	1181-1194	14
α-helix	1204-1214	11
α-helix	1216-1224	9
α-helix	1238-1242	5
α-helix	1253-1265	13
α-helix	1267-1270	4
α-helix	1278-1281	4
α-helix	1288	1
α-helix	1289-1293	5
α-helix	1294-1300	7
α-helix	1324	1
α-helix	1325-1330	6
α-helix	1331-1344	14
α-helix	1345-1350	6
α-helix	1356-1359	4
α-helix	1367-1377	11
α-helix	1379-1381	3
α-helix	1384-1386	3
α-helix	1389-1407	19
α-helix	1413-1416	4
α-helix	1428-1431	4
α-helix	1432-1434	3
α-helix	1446-1461	16
α-helix	1464-1467	4
α-helix	1477-1482	6
α-helix	1483-1488	6
α-helix	1499-1504	6
α-helix	1505-1519	15
α-helix	1525-1532	8
β-strand	1537-1538	2	30
β-strand	1553-1554	2	30
α-helix	1555-1562	8
α-helix	1564-1572	9
α-helix	1575-1580	6
α-helix	1581-1585	5
α-helix	1590-1607	18
α-helix	1614-1624	11
α-helix	1626-1629	4
α-helix	1639-1656	18
α-helix	1668-1678	11
α-helix	1686-1699	14
α-helix	1707-1721	15
α-helix	1726-1728	3
β-strand	1731	1	31
β-strand	1733	1	31
α-helix	1734-1751	18
α-helix	1756-1766	11
β-strand	1767	1	32
β-strand	1769	1	32
α-helix	1775-1787	13
α-helix	1791-1806	16
α-helix	1813-1819	7
α-helix	1820-1824	5
α-helix	1825-1828	4
α-helix	1836-1851	16
α-helix	1855-1857	3
α-helix	1861-1863	3
α-helix	1864-1875	12
α-helix	1878-1881	4
α-helix	1886-1889	4
β-strand	1893	1	33
β-strand	1907	1	33
α-helix	1911-1915	5
α-helix	1917-1924	8
α-helix	1934-1955	22
α-helix	1959-1963	5
α-helix	1974-1976	3
α-helix	2094-2105	12
α-helix	2121-2132	12
α-helix	2140-2151	12
α-helix	2154-2157	4
α-helix	2158-2160	3
α-helix	2161-2173	13
α-helix	2184-2200	17
α-helix	2206-2221	16
α-helix	2228-2243	16
α-helix	2253-2261	9
α-helix	2271-2282	12
α-helix	2296-2305	10
α-helix	2306-2308	3
α-helix	2313-2332	20
α-helix	2338-2353	16
α-helix	2357-2368	12
α-helix	2375-2385	11
α-helix	2392-2402	11
α-helix	2411-2417	7
α-helix	2420-2423	4
α-helix	2429-2442	14
α-helix	2443-2445	3
α-helix	2448-2458	11
α-helix	2459-2463	5
α-helix	2467-2484	18
α-helix	2493-2508	16
α-helix	2509-2511	3
α-helix	2515-2526	12
α-helix	2535-2542	8
α-helix	2548-2550	3
α-helix	2551-2563	13
α-helix	2564-2568	5
β-strand	2575	1	34
β-strand	2586-2587	2	35
α-helix	2725-2728	4
α-helix	2736-2767	32
β-strand	2777-2778	2	35
β-strand	2786	1	34
α-helix	2788-2798	11
α-helix	2802-2819	18
α-helix	2820-2822	3
α-helix	2826-2846	21
α-helix	2852-2863	12
α-helix	2868-2870	3
α-helix	2873-2882	10
α-helix	2886-2899	14
α-helix	2920-2932	13
α-helix	2936-2943	8
α-helix	2952-2961	10
α-helix	2965-2977	13
α-helix	2985-2987	3
α-helix	2988-3004	17
α-helix	3008-3017	10
α-helix	3027-3032	6
α-helix	3034-3053	20
α-helix	3060-3068	9
α-helix	3072-3081	10
α-helix	3083-3092	10
α-helix	3096-3116	21
α-helix	3122-3146	25
α-helix	3148-3151	4
α-helix	3155-3165	11
α-helix	3176-3196	21
α-helix	3228-3248	21
α-helix	3252-3266	15
α-helix	3270-3288	19
α-helix	3295-3300	6
α-helix	3304-3307	4
α-helix	3311-3313	3
α-helix	3320-3343	24
α-helix	3348-3351	4
α-helix	3357-3363	7
α-helix	3372-3392	21
α-helix	3409-3427	19
α-helix	3433-3439	7
α-helix	3442-3452	11
α-helix	3453-3455	3
α-helix	3459-3464	6
α-helix	3465-3467	3
α-helix	3468-3474	7
α-helix	3477-3479	3
α-helix	3480-3483	4
α-helix	3487-3489	3
α-helix	3492-3496	5
α-helix	3499-3504	6
α-helix	3511-3524	14
α-helix	3526-3537	12
α-helix	3546-3560	15
α-helix	3567-3577	11
α-helix	3584-3596	13
α-helix	3600-3602	3
α-helix	3603-3613	11
α-helix	3614-3618	5
α-helix	3627-3635	9
α-helix	3638-3642	5
α-helix	3646-3652	7
α-helix	3660-3671	12
α-helix	3676-3678	3
α-helix	3685-3689	5
β-strand	3700	1	36
α-helix	3701	1
α-helix	3713-3715	3
β-strand	3718	1	36
β-strand	3719-3722	4	37
β-strand	3728	1	37
β-strand	3736-3742	7	37
β-strand	3746-3754	9	37
α-helix	3759-3775	17
α-helix	3779-3782	4
β-strand	3797	1	37
β-strand	3800-3804	5	37
α-helix	3805	1
β-strand	3810-3811	2	38
α-helix	3812-3819	8
α-helix	3822-3829	8
α-helix	3839-3842	4
α-helix	3855-3861	7
α-helix	3864-3875	12
α-helix	3879	1
α-helix	3882-3890	9
β-strand	3891	1	28
α-helix	3894-3917	24
β-strand	3928-3931	4	38
β-strand	3936-3939	4	38
α-helix	3948-3951	4
α-helix	3965-3970	6
α-helix	3979-3992	14
α-helix	3995-4001	7
α-helix	4002-4004	3
α-helix	4039-4051	13
β-strand	4054	1	39
α-helix	4056-4065	10
α-helix	4068-4070	3
α-helix	4074-4081	8
β-strand	4096	1	39
α-helix	4100-4112	13
α-helix	4114-4117	4

4 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
Protein PAXX	S, T	protein	204	Homo sapiens	Q9BUH6 (AlphaFold model)
X-ray repair cross-complementing protein 6	A, J	protein	609	Homo sapiens	P12956 (AlphaFold model)
X-ray repair cross-complementing protein 5	B, K	protein	732	Homo sapiens	P13010 (AlphaFold model)
DNA-dependent protein kinase catalytic subunit	C, L	protein	4128	Homo sapiens	P78527
PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit -- Unknown region	Q, R	protein	20	Homo sapiens
DNA (31-mer)	D, M	DNA	31	Homo sapiens
DNA (30-mer)	E, N	DNA	30	Homo sapiens
Non-homologous end-joining factor 1	H, I	protein	299	Homo sapiens	Q9H9Q4
DNA repair protein XRCC4	F, G, O, P	protein	336	Homo sapiens	Q13426
DNA ligase 4	X, Y	protein	911	Homo sapiens	P49917

Sequence of entity 1 (S, T), FASTA

>8EZA_1 Protein PAXX (chains S, T)
MDPLSPPLCTLPPGPEPPRFVCYCEGEESGEGDRGGFNLYVTDAAELWSTCFTPDSLAAL
KARFGLSAAEDITPRFRAACEQQAVALTLQEDRASLTLSGGPSALAFDLSKVPGPEAAPR
LRALTLGLAKRVWSLERRLAAAEETAVSPRKSPRPAGPQLFLPDPDPQRGGPGPGVRRRC
PGESLINPGFKSKKPAGGVDFDET

Sequence of entity 2 (A, J), FASTA

>8EZA_2 X-ray repair cross-complementing protein 6 (chains A, J)
MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPF
DMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELD
QFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDS
AKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLE
DLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKT
RTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHH
YLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEEL
DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFEN
PVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKV
TKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELL
EALTKHFQD

Sequence of entity 3 (B, K), FASTA

>8EZA_3 X-ray repair cross-complementing protein 5 (chains B, K)
MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFG
TDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQH
ETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGD
GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKI
ERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDD
DETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQ
VLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLV
YVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTT
KIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLI
EAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENFRV
LVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLK
ALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAVFE
EGGDVDDLLDMI

Sequence of entity 4 (C, L), FASTA

>8EZA_4 DNA-dependent protein kinase catalytic subunit (chains C, L)
MAGSGAGVRCSLLRLQETLSAADRCGAALAGHQLIRGLGQECVLSSSPAVLALQTSLVFS
RDFGLLVFVRKSLNSIEFRECREEILKFLCIFLEKMGQKIAPYSVEIKNTCTSVYTKDRA
AKCKIPALDLLIKLLQTFRSSRLMDEFKIGELFSKFYGELALKKKIPDTVLEKVYELLGL
LGEVHPSEMINNAENLFRAFLGELKTQMTSAVREPKLPVLAGCLKGLSSLLCNFTKSMEE
DPQTSREIFNFVLKAIRPQIDLKRYAVPSAGLRLFALHASQFSTCLLDNYVSLFEVLLKW
CAHTNVELKKAALSALESFLKQVSNMVAKNAEMHKNKLQYFMEQFYGIIRNVDSNNKELS
IAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTQTDTGDDRVYQMPSFLQSVASV
LLYLDTVPEVYTPVLEHLVVMQIDSFPQYSPKMQLVCCRAIVKVFLALAAKGPVLRNCIS
TVVHQGLIRICSKPVVLPKGPESESEDHRASGEVRTGKWKVPTYKDYVDLFRHLLSSDQM
MDSILADEAFFSVNSSSESLNHLLYDEFVKSVLKIVEKLDLTLEIQTVGEQENGDEAPGV
WMIPTSDPAANLHPAKPKDFSAFINLVEFCREILPEKQAEFFEPWVYSFSYELILQSTRL
PLISGFYKLLSITVRNAKKIKYFEGVSPKSLKHSPEDPEKYSCFALFVKFGKEVAVKMKQ
YKDELLASCLTFLLSLPHNIIELDVRAYVPALQMAFKLGLSYTPLAEVGLNALEEWSIYI
DRHVMQPYYKDILPCLDGYLKTSALSDETKNNWEVSALSRAAQKGFNKVVLKHLKKTKNL
SSNEAISLEEIRIRVVQMLGSLGGQINKNLLTVTSSDEMMKSYVAWDREKRLSFAVPFRE
MKPVIFLDVFLPRVTELALTASDRQTKVAACELLHSMVMFMLGKATQMPEGGQGAPPMYQ
LYKRTFPVLLRLACDVDQVTRQLYEPLVMQLIHWFTNNKKFESQDTVALLEAILDGIVDP
VDSTLRDFCGRCIREFLKWSIKQITPQQQEKSPVNTKSLFKRLYSLALHPNAFKRLGASL
AFNNIYREFREEESLVEQFVFEALVIYMESLALAHADEKSLGTIQQCCDAIDHLCRIIEK
KHVSLNKAKKRRLPRGFPPSASLCLLDLVKWLLAHCGRPQTECRHKSIELFYKFVPLLPG
NRSPNLWLKDVLKEEGVSFLINTFEGGGCGQPSGILAQPTLLYLRGPFSLQATLCWLDLL
LAALECYNTFIGERTVGALQVLGTEAQSSLLKAVAFFLESIAMHDIIAAEKCFGTGAAGN
RTSPQEGERYNYSKCTVVVRIMEFTTTLLNTSPEGWKLLKKDLCNTHLMRVLVQTLCEPA
SIGFNIGDVQVMAHLPDVCVNLMKALKMSPYKDILETHLREKITAQSIEELCAVNLYGPD
AQVDRSRLAAVVSACKQLHRAGLLHNILPSQSTDLHHSVGTELLSLVYKGIAPGDERQCL
PSLDLSCKQLASGLLELAFAFGGLCERLVSLLLNPAVLSTASLGSSQGSVIHFSHGEYFY
SLFSETINTELLKNLDLAVLELMQSSVDNTKMVSAVLNGMLDQSFRERANQKHQGLKLAT
TILQHWKKCDSWWAKDSPLETKMAVLALLAKILQIDSSVSFNTSHGSFPEVFTTYISLLA
DTKLDLHLKGQAVTLLPFFTSLTGGSLEELRRVLEQLIVAHFPMQSREFPPGTPRFNNYV
DCMKKFLDALELSQSPMLLELMTEVLCREQQHVMEELFQSSFRRIARRGSCVTQVGLLES
VYEMFRKDDPRLSFTRQSFVDRSLLTLLWHCSLDALREFFSTIVVDAIDVLKSRFTKLNE
STFDTQITKKMGYYKILDVMYSRLPKDDVHAKESKINQVFHGSCITEGNELTKTLIKLCY
DAFTENMAGENQLLERRRLYHCAAYNCAISVICCVFNELKFYQGFLFSEKPEKNLLIFEN
LIDLKRRYNFPVEVEVPMERKKKYIEIRKEAREAANGDSDGPSYMSSLSYLADSTLSEEM
SQFDFSTGVQSYSYSSQDPRPATGRFRRREQRDPTVHDDVLELEMDELNRHECMAPLTAL
VKHMHRSLGPPQGEEDSVPRDLPSWMKFLHGKLGNPIVPLNIRLFLAKLVINTEEVFRPY
AKHWLSPLLQLAASENNGGEGIHYMVVEIVATILSWTGLATPTGVPKDEVLANRLLNFLM
KHVFHPKRAVFRHNLEIIKTLVECWKDCLSIPYRLIFEKFSGKDPNSKDNSVGIQLLGIV
MANDLPPYDPQCGIQSSEYFQALVNNMSFVRYKEVYAAAAEVLGLILRYVMERKNILEES
LCELVAKQLKQHQNTMEDKFIVCLNKVTKSFPPLADRFMNAVFFLLPKFHGVLKTLCLEV
VLCRVEGMTELYFQLKSKDFVQVMRHRDDERQKVCLDIIYKMMPKLKPVELRELLNPVVE
FVSHPSTTCREQMYNILMWIHDNYRDPESETDNDSQEIFKLAKDVLIQGLIDENPGLQLI
IRNFWSHETRLPSNTLDRLLALNSLYSPKIEVHFLSLATNFLLEMTSMSPDYPNPMFEHP
LSECEFQEYTIDSDWRFRSTVLTPMFVETQASQGTLQTRTQEGSLSARWPVAGQIRATQQ
QHDFTLTQTADGRSSFDWLTGSSTDPLVDHTSPSSDSLLFAHKRSERLQRAPLKSVGPDF
GKKRLGLPGDEVDNKVKGAAGRTDLLRLRRRFMRDQEKLSLMYARKGVAEQKREKEIKSE
LKMKQDAQVVLYRSYRHGDLPDIQIKHSSLITPLQAVAQRDPIIAKQLFSSLFSGILKEM
DKFKTLSEKNNITQKLLQDFNRFLNTTFSFFPPFVSCIQDISCQHAALLSLDPAAVSAGC
LASLQQPVGIRLLEEALLRLLPAELPAKRVRGKARLPPDVLRWVELAKLYRSIGEYDVLR
GIFTSEIGTKQITQSALLAEARSDYSEAAKQYDEALNKQDWVDGEPTEAEKDFWELASLD
CYNHLAEWKSLEYCSTASIDSENPPDLNKIWSEPFYQETYLPYMIRSKLKLLLQGEADQS
LLTFIDKAMHGELQKAILELHYSQELSLLYLLQDDVDRAKYYIQNGIQSFMQNYSSIDVL
LHQSRLTKLQSVQALTEIQEFISFISKQGNLSSQVPLKRLLNTWTNRYPDAKMDPMNIWD
DIITNRCFFLSKIEEKLTPLPEDNSMNVDQDGDPSDRMEVQEQEEDISSLIRSCKFSMKM
KMIDSARKQNNFSLAMKLLKELHKESKTRDDWLVSWVQSYCRLSHCRSRSQGCSEQVLTV
LKTVSLLDENNVSSYLSKNILAFRDQNILLGTTYRIIANALSSEPACLAEIEEDKARRIL
ELSGSSSEDSEKVIAGLYQRAFQHLSEAVQAAEEEAQPPSWSCGPAAGVIDAYMTLADFC
DQQLRKEEENASVIDSAELQAYPALVVEKMLKALKLNSNEARLKFPRLLQIIERYPEETL
SLMTKEISSVPCWQFISWISHMVALLDKDQAVAVQHSVEEITDNYPQAIVYPFIISSESY
SFKDTSTGHKNKEFVARIKSKLDQGGVIQDFINALDQLSNPELLFKDWSNDVRAELAKTP
VNKKNIEKMYERMYAALGDPKAPGLGAFRRKFIQTFGKEFDKHFGKGGSKLLRMKLSDFN
DITNMLLLKMNKDSKPPGNLKECSPWMSDFKVEFLRNELEIPGQYDGRGKPLPEYHVRIA
GFDERVTVMASLRRPKRIIIRGHDEREHPFLVKGGEDLRQDQRVEQLFQVMNGILAQDSA
CSQRALQLRTYSVVPMTSRLGLIEWLENTVTLKDLLLNTMSQEEKAAYLSDPRAPPCEYK
DWLTKMSGKHDVGAYMLMYKGANRTETVTSFRKRESKVPADLLKRAFVRMSTSPEAFLAL
RSHFASSHALICISHWILGIGDRHLNNFMVAMETGGVIGIDFGHAFGSATQFLPVPELMP
FRLTRQFINLMLPMKETGLMYSIMVHALRAFRSDPGLLTNTMDVFVKEPSFDWKNFEQKM
LKKGGSWIQEINVAEKNWYPRQKICYAKRKLAGANPAVITCDELLLGHEKAPAFRDYVAV
ARGSKDHNIRAQEPESGLSEETQVKCLMDQATDPNILGRTWEGWEPWM

Sequence of entity 5 (Q, R), FASTA

>8EZA_5 PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit -- Unknown region (chains Q, R)
XXXXXXXXXXXXXXXXXXXX

Sequence of entity 6 (D, M), FASTA

>8EZA_6 DNA (31-MER) (chains D, M)
TCTAAGAACTCTGATGTCAGTAGATTACACT

Sequence of entity 7 (E, N), FASTA

>8EZA_7 DNA (30-MER) (chains E, N)
GTGTAATCTACTGACATCAGAGTTCTTAGA

Sequence of entity 8 (H, I), FASTA

>8EZA_8 Non-homologous end-joining factor 1 (chains H, I)
MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKE
LNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWN
FHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLK
TEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQVGQKHQGAGDPHT
SNSASLQGIDSQCVNQPEQLVSSAPTLSAPEKESTGTSGPLQRPQLSKVKRKKPRGLFS

Sequence of entity 9 (F, G, O, P), FASTA

>8EZA_9 DNA repair protein XRCC4 (chains F, G, O, P)
MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMA
MEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPA
EVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRF
ILVLNEKKTKIRSLHNKLLNAAQEREKDIKQEGETAICSEMTADRDPVYDESTDEESENQ
TDLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQRMQRNLGTEPKMAPQENQLQEKENSR
PDSSLPETSKKEHISAENMSLETLRNSSPEDLFDEI

Sequence of entity 10 (X, Y), FASTA

>8EZA_10 DNA ligase 4 (chains X, Y)
MAASQTSQTVASHVPFADLCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKNHKDV
TDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPTGTHG
DAGDFAMIAYFVLKPRCLQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLITQSSA
LEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVCRQLHDPSVGLSDISI
TLFSAFKPMLAAIADIEHIEKDMKHQSFYIETKLDGERMQMHKDGDVYKYFSRNGYNYTD
QFGASPTEGSLTPFIHNAFKADIQICILDGEMMAYNPNTQTFMQKGTKFDIKRMVEDSDL
QTCYCVFDVLMVNNKKLGHETLRKRYEILSSIFTPIPGRIEIVQKTQAHTKNEVIDALNE
AIDKREEGIMVKQPLSIYKPDKRGEGWLKIKPEYVSGLMDELDILIVGGYWGKGSRGGMM
SHFLCAVAEKPPPGEKPSVFHTLSRVGSGCTMKELYDLGLKLAKYWKPFHRKAPPSSILC
GTEKPEVYIEPCNSVIVQIKAAEIVPSDMYKTGCTLRFPRIEKIRDDKEWHECMTLDDLE
QLRGKASGKLASKHLYIGGDDEPQEKKRKAAPKMKKVIGIIEHLKAPNLTNVNKISNIFE
DVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGPDTYCVIAGSENIRVKNIILSNKHDV
VKPAWLLECFKTKSFVPWQPRFMIHMCPSTKEHFAREYDCYGDSYFIDTDLNQLKEVFSG
IKNSNEQTPEEMASLIADLEYRYSWDCSPLSMFRRHTVYLDSYAVINDLSTKNEGTRLAI
KALELRFHGAKVVSCLAEGVSHVIIGEDHSRVADFKAFRRTFKRKFKILKESWVTDSIDK
CELQEENQYLI

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ. Chen, S., Vogt, A., Lee, L. et al. Sci Adv (2023) 9:eadg2838-eadg2838. DOI 10.1126/sciadv.adg2838 · PubMed

Other PDB entries of the same protein (UniProt Q9BUH6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3WTD 2.35 Å, Structure of PAXX
4WJA 2.6 Å, Crystal Structure of PAXX
7ZYG 2.68 Å, CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF
7ZWA 2.8 Å, CryoEM structure of Ku heterodimer bound to DNA and PAXX
9CQ3 2.8 Å, The gap-filling complex with Pol mu engaged in the NHEJ pathway
9GYF 2.8 Å, Ku70/80 with PAXX peptide mutation K193R
9N81 2.8 Å, A gap-filling complex with Pol mu engaged in the NHEJ Pathway
8ASC 2.95 Å, Ku70/80 binds to the Ku-binding motif of PAXX
9CQ6 3.1 Å, The ligation complex in the NHEJ pathway
9N83 3.1 Å, The ligation complex in the NHEJ pathway
9N82 3.3 Å, The ligation (AMP-Lys) complex in the NHEJ pathway
9CQC 3.4 Å, The ligation complex like in the NHEJ pathway

Browse structure collections

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