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
Browse structure collections
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