9CQC: The ligation complex like in the NHEJ pathway

The ligation complex like in the NHEJ pathway. Determined by electron microscopy at 3.4 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 18
Atoms: 39,149
Mol. weight: 855.33 kDa
Ligands: DZ4
Released: 23 Apr 2025

Explore 9CQC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CQC contains 183 α-helices and 225 β-strands across 14 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: 21 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	35-43	9	28
α-helix	46-48	3
α-helix	59-77	19
β-strand	82-88	7	28
β-strand	94	1	28
β-strand	102-109	8	28
α-helix	113-119	7
α-helix	120-122	3
α-helix	125-135	11
α-helix	143-156	14
β-strand	161-170	10	28
α-helix	180-196	17
β-strand	199-204	6	28
β-strand	211-212	2	29
α-helix	217-219	3
β-strand	231-232	2	29
α-helix	235-236	2
α-helix	238-243	6
β-strand	257-262	6	30
β-strand	269-274	6	30
β-strand	277	1	31
α-helix	281-285	5
β-strand	286-289	4	32
β-strand	295	1	32
β-strand	297-302	6	33
β-strand	303	1	34
β-strand	310	1	34
α-helix	313-315	3
β-strand	316-321	6	35
β-strand	326-329	4	35
α-helix	331-337	7
β-strand	344-352	9	30
α-helix	353-355	3
β-strand	366-370	5	30
β-strand	375-376	2	36
α-helix	378-392	15
β-strand	394-401	8	30
β-strand	409-416	8	30
β-strand	419-420	2	37
β-strand	426-428	3	37
β-strand	431-436	6	30
α-helix	437-438	2
β-strand	443	1	38
α-helix	453-455	3
α-helix	456-468	13
β-strand	470	1	38
β-strand	471	1	27
α-helix	481-495	15
α-helix	511-517	7
α-helix	521-529	9

Chain A: 21 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	35-43	9	1
α-helix	46-48	3
α-helix	59-77	19
β-strand	82-88	7	1
β-strand	94	1	1
β-strand	102-109	8	1
α-helix	113-120	8
α-helix	125-135	11
α-helix	143-156	14
β-strand	161-169	9	1
α-helix	180-196	17
β-strand	198-202	5	1
α-helix	204-206	3
β-strand	211-212	2	2
α-helix	217-219	3
α-helix	227-229	3
β-strand	231-232	2	2
α-helix	238-243	6
β-strand	257-262	6	3
β-strand	268-274	7	3
β-strand	277	1	4
α-helix	282-285	4
β-strand	286-289	4	5
β-strand	295	1	5
β-strand	296-304	9	6
β-strand	310	1	6
β-strand	316-322	7	7
β-strand	325-329	5	7
α-helix	331-337	7
β-strand	344-352	9	3
α-helix	353-355	3
β-strand	366-370	5	3
β-strand	375-376	2	8
α-helix	378-392	15
β-strand	394-401	8	3
β-strand	409-416	8	3
β-strand	419-421	3	9
β-strand	425-428	4	9
β-strand	431-436	6	3
α-helix	437-438	2
β-strand	443	1	10
α-helix	445-448	4
α-helix	456-468	13
β-strand	470	1	10
β-strand	471	1	11
α-helix	481-495	15
α-helix	502-504	3
α-helix	511-518	8
α-helix	521-529	9

Chain b: 23 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	39
α-helix	18-21	4
α-helix	30-47	18
β-strand	53-59	7	39
β-strand	65	1	39
β-strand	77-84	8	39
α-helix	88-95	8
α-helix	107-121	15
β-strand	129-135	7	39
α-helix	147-157	11
β-strand	160-165	6	39
α-helix	199-216	18
α-helix	217-223	7
β-strand	224-226	3	39
α-helix	227-230	4
α-helix	238-240	3
α-helix	243-246	4
β-strand	247-252	6	38
β-strand	258-268	11	38
β-strand	277-280	4	35
β-strand	291-296	6	33
β-strand	304	1	33
α-helix	307-309	3
β-strand	310-315	6	32
β-strand	320-322	3	32
α-helix	325-331	7
β-strand	339-347	9	38
α-helix	348-350	3
α-helix	353-355	3
β-strand	360-366	7	38
α-helix	372-387	16
β-strand	389-396	8	38
α-helix	402-403	2
β-strand	404-412	9	38
β-strand	417-423	7	38
β-strand	430	1	31
α-helix	442-444	3
α-helix	448-460	13
β-strand	462	1	30
β-strand	464-466	3	40
β-strand	473-475	3	40
α-helix	479-481	3
α-helix	485-499	15
α-helix	504-509	6
α-helix	510-516	7
α-helix	520-536	17
β-strand	540-541	2	36

Chain B: 26 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	12
α-helix	18-21	4
α-helix	30-47	18
β-strand	52-59	8	12
β-strand	65	1	12
α-helix	67-69	3
β-strand	77-84	8	12
α-helix	88-95	8
α-helix	107-122	16
β-strand	129-135	7	12
α-helix	144-146	3
α-helix	147-157	11
β-strand	160-165	6	12
α-helix	199-215	17
α-helix	219-223	5
β-strand	224-226	3	12
α-helix	227-230	4
α-helix	235-237	3
α-helix	244-246	3
β-strand	247-252	6	10
β-strand	258-268	11	10
β-strand	277-280	4	7
α-helix	286-288	3
β-strand	289-297	9	6
β-strand	304-305	2	6
β-strand	310-315	6	5
β-strand	320-322	3	5
α-helix	325-331	7
β-strand	339-347	9	10
α-helix	353-355	3
β-strand	360-366	7	10
α-helix	367	1
α-helix	371-387	17
β-strand	389-396	8	10
α-helix	402-403	2
β-strand	404-412	9	10
β-strand	417-423	7	10
β-strand	430	1	4
α-helix	448-460	13
β-strand	462	1	3
β-strand	464-467	4	13
β-strand	472-475	4	13
α-helix	479-481	3
α-helix	483-484	2
α-helix	485-499	15
α-helix	504-509	6
α-helix	510-515	6
α-helix	520-524	5
α-helix	527-536	10
β-strand	540-541	2	8

Chain c: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	0-10	11
β-strand	14-17	4	41
β-strand	22-30	9	41
β-strand	33-39	7	41
β-strand	44-50	7	41
α-helix	51-62	12
β-strand	65-66	2	42
α-helix	69-85	17
β-strand	93-98	6	43
β-strand	104-112	9	43
β-strand	115-123	9	43
β-strand	124-125	2	41
α-helix	126-127	2
α-helix	128-131	4
α-helix	132-136	5
α-helix	137-169	33
α-helix	182-184	3
α-helix	186-196	11
α-helix	198-201	4
α-helix	208-213	6
α-helix	216-228	13

Chain C: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	1-9	9
β-strand	14-18	5	14
β-strand	21-30	10	14
β-strand	33-39	7	14
β-strand	44-50	7	14
α-helix	51-61	11
β-strand	65-66	2	15
α-helix	69-85	17
β-strand	94-99	6	16
β-strand	104-112	9	16
β-strand	115-123	9	16
β-strand	124-125	2	14
α-helix	126-127	2
α-helix	128-131	4
α-helix	132-136	5
α-helix	137-169	33
α-helix	172-174	3
α-helix	177-179	3
α-helix	182-184	3
α-helix	186-196	11
α-helix	198-201	4
α-helix	208-213	6
α-helix	215-226	12

Chain d: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	44
β-strand	18-24	7	44
β-strand	31-37	7	44
β-strand	42-48	7	44
α-helix	49-59	11
α-helix	63-70	8
α-helix	71-76	6
β-strand	85-89	5	45
β-strand	94-101	8	45
β-strand	104-107	4	45
β-strand	111-112	2	45
α-helix	113	1
β-strand	114-115	2	44
α-helix	120-200	81

Chain D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	17
β-strand	18-24	7	17
α-helix	28-30	3
β-strand	33-37	5	17
β-strand	42-46	5	17
α-helix	49-59	11
α-helix	63-74	12
β-strand	83-89	7	18
β-strand	94-101	8	18
β-strand	104-112	9	18
β-strand	114-115	2	17
α-helix	119-200	82

6 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
X-ray repair cross-complementing protein 6	A, a	protein	612	Homo sapiens	P12956 (AlphaFold model)
X-ray repair cross-complementing protein 5	B, b	protein	732	Homo sapiens	P13010 (AlphaFold model)
Non-homologous end-joining factor 1	C, c	protein	302	Homo sapiens	Q9H9Q4 (AlphaFold model)
DNA repair protein XRCC4	D, E, d, e	protein	336	Homo sapiens	Q13426 (AlphaFold model)
DNA ligase 4	F, f	protein	914	Homo sapiens	P49917
Protein PAXX	G, H	protein	218	Homo sapiens	Q9BUH6
DNA (38-mer)	I	DNA	68	Homo sapiens
DNA (40-mer)	J	DNA	68	Homo sapiens
DNA (34-mer)	K	DNA	51	Homo sapiens
DNA (35-mer)	L	DNA	50	Homo sapiens

Sequence of entity 1 (A, a), FASTA

>9CQC_1 X-ray repair cross-complementing protein 6 (chains A, a)
GPVMSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDEL
TPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRIL
ELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHG
NDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESS
KLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVK
TKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLK
KHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQE
EELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDS
FENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPE
GKVTKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQ
ELLEALTKHFQD

Sequence of entity 2 (B, b), FASTA

>9CQC_2 X-ray repair cross-complementing protein 5 (chains B, b)
MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFG
TDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQH
ETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGD
GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKI
ERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDD
DETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQ
VLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLV
YVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTT
KIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLI
EAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENFRV
LVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLK
ALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAVFE
EGGDVDDLLDMI

Sequence of entity 3 (C, c), FASTA

>9CQC_3 Non-homologous end-joining factor 1 (chains C, c)
GPVMEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQR
AKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPF
YWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRD
RLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQVGQKHQGAGD
PHTSNSASLQGIDSQCVNQPEQLVSSAPTLSAPEKESTGTSGPLQRPQLSKVKRKKPRGL
FS

Sequence of entity 4 (D, E, d, e), FASTA

>9CQC_4 DNA repair protein XRCC4 (chains D, E, d, e)
MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMA
MEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPA
EVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRF
ILVLNEKKTKIRSLHNKLLNAAQEREKDIKQEGETAICSEMTADRDPVYDESTDEESENQ
TDLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQRMQRNLGTEPKMAPQENQLQEKENSR
PDSSLPETSKKEHISAENMSLETLRNSSPEDLFDEI

Sequence of entity 5 (F, f), FASTA

>9CQC_5 DNA ligase 4 (chains F, f)
GPVMAASQTSQTVASHVPFADLCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKNH
KDVTDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPTG
THGDAGDFAMIAYFVLKPRCLQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLITQ
SSALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVCRQLHDPSVGLSD
ISITLFSAFKPMLAAIADIEHIEKDMKHQSFYIETKLDGERMQMHKDGDVYKYFSRNGYN
YTDQFGASPTEGSLTPFIHNAFKADIQICILDGEMMAYNPNTQTFMQKGTKFDIKRMVED
SDLQTCYCVFDVLMVNNKKLGHETLRKRYEILSSIFTPIPGRIEIVQKTQAHTKNEVIDA
LNEAIDKREEGIMVKQPLSIYKPDKRGEGWLKIKPEYVSGLMDELDILIVGGYWGKGSRG
GMMSHFLCAVAEKPPPGEKPSVFHTLSRVGSGCTMKELYDLGLKLAKYWKPFHRKAPPSS
ILCGTEKPEVYIEPCNSVIVQIKAAEIVPSDMYKTGCTLRFPRIEKIRDDKEWHECMTLD
DLEQLRGKASGKLASKHLYIGGDDEPQEKKRKAAPKMKKVIGIIEHLKAPNLTNVNKISN
IFEDVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGPDTYCVIAGSENIRVKNIILSNK
HDVVKPAWLLECFKTKSFVPWQPRFMIHMCPSTKEHFAREYDCYGDSYFIDTDLNQLKEV
FSGIKNSNEQTPEEMASLIADLEYRYSWDCSPLSMFRRHTVYLDSYAVINDLSTKNEGTR
LAIKALELRFHGAKVVSCLAEGVSHVIIGEDHSRVADFKAFRRTFKRKFKILKESWVTDS
IDKCELQEENQYLI

Sequence of entity 6 (G, H), FASTA

>9CQC_6 Protein PAXX (chains G, H)
MGSSHHHHHHSQDPMDPLSPPLCTLPPGPEPPRFVCYCEGEESGEGDRGGFNLYVTDAAE
LWSTCFTPDSLAALKARFGLSAAEDITPRFRAACEQQAVALTLQEDRASLTLSGGPSALA
FDLSKVPGPEAAPRLRALTLGLAKRVWSLERRLAAAEETAVSPRKSPRPAGPQLFLPDPD
PQRGGPGPGVRRRCPGESLINPGFKSKKPAGGVDFDET

Sequence of entity 7 (I), FASTA

>9CQC_7 DNA (38-MER) (chains I)
CGCGCCCAGCTTTCCCAGCTAATAAACTAAAAACTATGCATGCTCTACTGCTTCTGATCT
AGTCGACT

Sequence of entity 8 (J), FASTA

>9CQC_8 DNA (40-MER) (chains J)
CGCGCCCAGCTTTCCCAGCTAATAAACTAAAAACATTCGTTCACGTGAGTTCCAGTACAA
GTCTAGTC

Sequence of entity 9 (K), FASTA

>9CQC_9 DNA (34-MER) (chains K)
GACTAGATCAGAAGCAGTAGAGCATGCATAGTTTTTAGTTTATTGGGCGCG

Sequence of entity 10 (L), FASTA

>9CQC_10 DNA (35-MER) (chains L)
GACTTGTACTGGAACTCACGTGAACGAATGTTTTTAGTTTATTGGGCGCG

Ligands and cofactors

ID	Name	Formula	Copies
DZ4	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphory…	C10 H17 N6 O11 P3	1

Primary citation

Dynamic assemblies and coordinated reactions of non-homologous end joining. Liu, L., Li, J., Cisneros-Aguirre, M. et al. Nature (2025) 643:847-854. DOI 10.1038/s41586-025-09078-9 · PubMed

Other PDB entries of the same protein (UniProt P12956 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8AG4 2.46 Å, Vaccinia C16 protein bound to Ku70/Ku80
1JEY 2.5 Å, Crystal Structure of the Ku heterodimer bound to DNA
3RZX 2.61 Å, Mouse importin alpha-Ku70 NLS peptide complex
7ZYG 2.68 Å, CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF
1JEQ 2.7 Å, Crystal Structure of the Ku Heterodimer
7ZVT 2.74 Å, CryoEM structure of Ku heterodimer bound to DNA
6ERH 2.8 Å, Complex of XLF and heterodimer Ku bound to DNA
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
6ERG 2.9 Å, Complex of XLF and heterodimer Ku bound to DNA

Browse structure collections

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