› 6oen

Electron Microscopy
4.3Å resolution

Cryo-EM structure of mouse RAG1/2 PRC complex (DNA1)

Released:
DOI: 10.2210/pdb6oen/pdb
PDB entry 6oen coloured by chain, front view.
PDB entry 6oen coloured by chain, side view.
PDB entry 6oen coloured by chain, top view.
Source organisms:
Primary publication:
Cutting antiparallel DNA strands in a single active site.
Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, Gellert M
Nat Struct Mol Biol 27 119-126 (2020)
PMID: 32015552
Related structures: EMD-20031

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-120385 (preferred)
Entry contents:
3 distinct polypeptide molecules
4 distinct DNA molecules
Macromolecules (7 distinct):
V(D)J recombination-activating protein 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 1040 amino acids
Theoretical weight: 119.39 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: P15919 (Residues: 1-1040; Coverage: 100%)
Gene name: Rag1
Sequence domains:
V(D)J recombination-activating protein 2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 527 amino acids
Theoretical weight: 59.14 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: P21784 (Residues: 1-527; Coverage: 100%)
Gene names: Rag-2, Rag2
Sequence domains:
High mobility group protein B1 Chains: H, N
Molecule details ›
Chains: H, N
Length: 163 amino acids
Theoretical weight: 18.9 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P09429 (Residues: 1-163; Coverage: 76%)
Gene names: HMG1, HMGB1
Sequence domains:
DNA (57-MER) Chain: G
Molecule details ›
Chain: G
Length: 61 nucleotides
Theoretical weight: 18.81 KDa
DNA (46-MER) Chain: I
Molecule details ›
Chain: I
Length: 50 nucleotides
Theoretical weight: 15.28 KDa
DNA (46-MER) Chain: F
Molecule details ›
Chain: F
Length: 50 nucleotides
Theoretical weight: 15.53 KDa
DNA (57-MER) Chain: J
Molecule details ›
Chain: J
Length: 61 nucleotides
Theoretical weight: 18.79 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.3Å
Relevant EMDB volumes: EMD-20031
Expression systems:
  • Homo sapiens
  • Escherichia coli BL21

Quick links

Citations

6 review citations

The molecular basis and disease relevance of non-homologous DNA end joining.
Zhao et al. (2020)
5 more

1 mention without citation

Cutting antiparallel DNA strands in a single active site.
Chen et al. (2020)