6dbx

Electron Microscopy
4.2Å resolution

Cryo-EM structure of RAG in complex with 12-RSS substrate DNA

Released:
Primary publication:
DNA melting initiates the RAG catalytic pathway.
Nat. Struct. Mol. Biol. 25 732-742 (2018)
PMID: 30061602
Related structures: EMD-7853

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:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 1159 amino acids
Theoretical weight: 131.16 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P0AEX9 (Residues: 15-15, 29-392; Coverage: 95%)
  • Canonical: O13033 (Residues: 271-1031; Coverage: 72%)
Gene names: JW3994, b4034, malE, rag1
Sequence domains:
V(D)J recombination-activating protein 2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 533 amino acids
Theoretical weight: 59.44 KDa
Source organism: Danio rerio
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O13034 (Residues: 1-530; Coverage: 100%)
Gene names: rag-2, rag2
Sequence domains:
Forward strand of 12-RSS substrate DNA Chain: E
Molecule details ›
Chain: E
Length: 50 nucleotides
Theoretical weight: 15.36 KDa
Reverse strand of 12-RSS substrate DNA Chain: F
Molecule details ›
Chain: F
Length: 50 nucleotides
Theoretical weight: 15.44 KDa

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.2Å
Relevant EMDB volumes: EMD-7853
Expression system: Spodoptera frugiperda