10YF: DNA Ligase IIIa
DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite). Determined by electron microscopy at 3.0 Å resolution. Released 18 Mar 2026.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 12
- Atoms
- 13,644
- Mol. weight
- 199.49 kDa
- Ligands
- AMP
- Released
- 18 Mar 2026
Explore 10YF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
10YF contains 47 α-helices and 36 β-strands across 9 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 | 45-48 | 4 | |
| α-helix | 52-56 | 5 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-35 | 8 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101 | 1 | 6 |
| α-helix | 102 | 1 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 5 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-122 | 18 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-92 | 10 | |
| β-strand | 97 | 1 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
| α-helix | 113-115 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 10 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 9 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-123 | 19 | |
1 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 |
|---|
| Histone H3.2 | A, E | protein | 96 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | B, F | protein | 80 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-H | C, G | protein | 107 | Homo sapiens | Q96KK5 (AlphaFold model) |
| Histone H2B type 2-F | D, H | protein | 92 | Homo sapiens | Q5QNW6 (AlphaFold model) |
| 601 I strand (non-damaged strand) | I | DNA | 147 | synthetic construct | |
| 601 J strand (damaged strand 1) | J | DNA | 56 | synthetic construct | |
| 601 K strand (damaged strand 2) | K | DNA | 91 | synthetic construct | |
| DNA ligase 3 | L | protein | 208 | Homo sapiens | P49916 |
Sequence of entity 1 (A, E), FASTA
>10YF_1 Histone H3.2 (chains A, E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASE
AYLVGLFEDTNLAAIHAKRVTIMPKDIQLARRIRGE
Sequence of entity 2 (B, F), FASTA
>10YF_2 Histone H4 (chains B, F)
LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTV
TAMDVVYALKRQGRTLYGFG
Sequence of entity 3 (C, G), FASTA
>10YF_3 Histone H2A type 1-H (chains C, G)
RAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLP
Sequence of entity 4 (D, H), FASTA
>10YF_4 Histone H2B type 2-F (chains D, H)
RKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSR
EIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS
Sequence of entity 5 (I), FASTA
>10YF_5 601 I strand (non-damaged strand) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT
Sequence of entity 6 (J), FASTA
>10YF_6 601 J strand (damaged strand 1) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGG
Sequence of entity 7 (K), FASTA
>10YF_7 601 K strand (damaged strand 2) (chains K)
TTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCA
ATTGAGCGGCCTCGGCACCGGGATTCTCGAT
Sequence of entity 8 (L), FASTA
>10YF_8 DNA ligase 3 (chains L)
QASLMTPVQPMLAEACKSVEYAMKKCPNGMFSEIKYDGERVQVHKNGDHFSYFSRSLKPV
LPHKVAHFKDYIPQAFPGGHSMILDSEVLLIDNKTGKPLPFGTLGVHKKAAFQDANVCLF
VFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMFSEMKRVTKALDLADMITRVIQEG
LEGLVLKDVKGTYEPGKRHWLKVKKDYL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| AMP | Adenosine monophosphate | C10 H14 N5 O7 P | 1 |
Primary citation
Molecular basis of nick ligation in the nucleosome by DNA Ligase III alpha. Boesch, D.J., Martin, N.I., Kontor, C.A. et al. Nat Commun (2026). DOI 10.1038/s41467-026-77207-7
Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
- 2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
- 5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
- 6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
- 7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
- 5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
- 3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
- 4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
- 4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide
Browse structure collections
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