› 7lsy

Electron Microscopy
8.4Å resolution

NHEJ Short-range synaptic complex

Released:
DOI: 10.2210/pdb7lsy/pdb
PDB entry 7lsy coloured by chain, front view.
PDB entry 7lsy coloured by chain, side view.
PDB entry 7lsy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of long-range to short-range synaptic transition in NHEJ.
Chen S, Lee L, Naila T, Fishbain S, Wang A, Tomkinson AE, Lees-Miller SP, He Y
Nature 593 294-298 (2021)
PMID: 33854234
Related structures: EMD-23509

Function and Biology Details

Reaction catalysed: 
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero heptadecamer (preferred)
PDBe Complex ID:
PDB-CPX-121552 (preferred)
Entry contents:
5 distinct polypeptide molecules
5 distinct DNA molecules
Macromolecules (10 distinct):
X-ray repair cross-complementing protein 6 Chains: A, J
Molecule details ›
Chains: A, J
Length: 600 amino acids
Theoretical weight: 68.87 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: P12956 (Residues: 1-600; Coverage: 99%)
Gene names: G22P1, XRCC6
Sequence domains:
X-ray repair cross-complementing protein 5 Chains: B, K
Molecule details ›
Chains: B, K
Length: 732 amino acids
Theoretical weight: 82.81 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: P13010 (Residues: 1-732; Coverage: 100%)
Gene names: G22P2, XRCC5
Sequence domains:
DNA repair protein XRCC4 Chains: F, G, O, P
Molecule details ›
Chains: F, G, O, P
Length: 336 amino acids
Theoretical weight: 38.34 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: Q13426 (Residues: 1-336; Coverage: 100%)
Gene name: XRCC4
Sequence domains: DNA double-strand break repair and V(D)J recombination protein XRCC4
Non-homologous end-joining factor 1 Chains: H, I
Molecule details ›
Chains: H, I
Length: 299 amino acids
Theoretical weight: 33.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H9Q4 (Residues: 1-299; Coverage: 100%)
Gene names: NHEJ1, XLF
Sequence domains: XLF-Cernunnos, XRcc4-like factor, NHEJ component
DNA ligase 4 Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 911 amino acids
Theoretical weight: 104.12 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: P49917 (Residues: 1-911; Coverage: 100%)
Gene name: LIG4
Sequence domains:
DNA (26-MER) Chain: D
Molecule details ›
Chain: D
Length: 26 nucleotides
Theoretical weight: 7.94 KDa
DNA (5'-D(P*GP*TP*TP*CP*TP*TP*AP*GP*TP*AP*TP*AP*TP*A)-3') Chain: E
Molecule details ›
Chain: E
Length: 14 nucleotides
Theoretical weight: 4.28 KDa
DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*TP*AP*AP*GP*AP*AP*C)-3') Chain: M
Molecule details ›
Chain: M
Length: 14 nucleotides
Theoretical weight: 4.27 KDa
DNA (26-MER) Chain: N
Molecule details ›
Chain: N
Length: 26 nucleotides
Theoretical weight: 7.96 KDa
DNA (5'-D(P*CP*AP*AP*TP*GP*AP*AP*AP*CP*GP*GP*AP*AP*CP*AP*GP*TP*CP*AP*G)-3') Chain: V
Molecule details ›
Chain: V
Length: 20 nucleotides
Theoretical weight: 6.19 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 8.4Å
Relevant EMDB volumes: EMD-23509
Expression systems:
  • unidentified baculovirus
  • Escherichia coli

Quick links

Citations

17 review citations

Function and Molecular Mechanism of the DNA Damage Response in Immunity and Cancer Immunotherapy.
Ye et al. (2021)
16 more

3 mentions without citation

Structural analysis of the basal state of the Artemis:DNA-PKcs complex.
Watanabe et al. (2022)
2 more