9Q80: Ku70/80 with Ku70 linker and SAP domain

Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome. Determined by electron microscopy at 3.39 Å resolution. Released 14 Jan 2026.

Method: Electron microscopy
Resolution: 3.39 Å
Organism: Homo sapiens
Chains: 14
Atoms: 27,768
Mol. weight: 511.85 kDa
Released: 14 Jan 2026

Explore 9Q80 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q80 contains 119 α-helices and 117 β-strands across 12 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-54	10
α-helix	64-78	15
β-strand	83-84	2	40
α-helix	85	1
α-helix	86-113	28
β-strand	118-119	2	41
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	41
α-helix	50-75	26
β-strand	80-81	2	40
α-helix	83-92	10
β-strand	97-98	2	21

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	14
α-helix	46-72	27
β-strand	77-78	2	15
α-helix	79	1
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	16

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	15
α-helix	53-80	28
β-strand	85-86	2	14
α-helix	88-98	11
α-helix	101-120	20

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	17
α-helix	86-113	28
β-strand	119	1	18
α-helix	121-131	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	46	1	18
α-helix	50-75	26
β-strand	80-81	2	17
α-helix	83-92	10
β-strand	97-98	2	16

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	19
α-helix	46-72	27
β-strand	77-78	2	20
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	21

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	20
α-helix	53-80	28
β-strand	85-86	2	19
α-helix	88-98	11
α-helix	102-119	18

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
X-ray repair cross-complementing protein 6	K, M	protein	609	Homo sapiens	P12956 (AlphaFold model)
X-ray repair cross-complementing protein 5	L, N	protein	732	Homo sapiens	P13010 (AlphaFold model)
Histone H2AX	C, G	protein	143	Homo sapiens	P16104 (AlphaFold model)
Histone H2B type 1-J	D, H	protein	126	Homo sapiens	P06899 (AlphaFold model)
Histone H3.1	A, E	protein	136	Homo sapiens	P68431
Histone H4	B, F	protein	103	Homo sapiens	P62805
DNA	I	DNA	153	Homo sapiens
DNA	J	DNA	153	Homo sapiens

Sequence of entity 1 (K, M), FASTA

>9Q80_1 X-ray repair cross-complementing protein 6 (chains K, M)
MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPF
DMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELD
QFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDS
AKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLE
DLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKT
RTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHH
YLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEEL
DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFEN
PVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKV
TKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELL
EALTKHFQD

Sequence of entity 2 (L, N), FASTA

>9Q80_2 X-ray repair cross-complementing protein 5 (chains L, N)
MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFG
TDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQH
ETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGD
GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKI
ERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDD
DETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQ
VLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLV
YVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTT
KIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLI
EAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENFRV
LVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLK
ALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAVFE
EGGDVDDLLDMI

Sequence of entity 3 (C, G), FASTA

>9Q80_3 Histone H2AX (chains C, G)
MSGRGKTGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGHYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKK
TSATVGPKAPSGGKKATQASQEY

Sequence of entity 4 (D, H), FASTA

>9Q80_4 Histone H2B type 1-J (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 5 (A, E), FASTA

>9Q80_5 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 6 (B, F), FASTA

>9Q80_6 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 7 (I), FASTA

>9Q80_7 DNA (chains I)
ATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCT
TAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCT
CCAGGCACGTGTCAGATATATACATCCTGTGAT

Sequence of entity 8 (J), FASTA

>9Q80_8 DNA (chains J)
ATCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGT
TAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAA
TTGAGCGGCCTCGGCACCGGGATTCTCCAGGAT

Primary citation

Cryo-EM structures of NHEJ assemblies with nucleosomes. Hall, C., Frit, P., Kefala-Stavridi, A. et al. Nat Commun (2025) 17:648-648. DOI 10.1038/s41467-025-67376-2 · 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

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