› 6oes

Electron Microscopy
3.06Å resolution

Cryo-EM structure of mouse RAG1/2 STC complex (without NBD domain)

Released:
DOI: 10.2210/pdb6oes/pdb
PDB entry 6oes coloured by chain, front view.
PDB entry 6oes coloured by chain, side view.
PDB entry 6oes coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
How mouse RAG recombinase avoids DNA transposition.
Chen X, Cui Y, Wang H, Zhou ZH, Gellert M, Yang W
Nat Struct Mol Biol 27 127-133 (2020)
PMID: 32015553
Related structures: EMD-20036

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)
Assembly name:
PDBe Complex ID:
PDB-CPX-120390 (preferred)
Entry contents:
2 distinct polypeptide molecules
5 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:
DNA (35-MER) Chain: F
Molecule details ›
Chain: F
Length: 50 nucleotides
Theoretical weight: 15.52 KDa
DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3') Chains: I, J
Molecule details ›
Chains: I, J
Length: 15 nucleotides
Theoretical weight: 4.58 KDa
DNA (34-MER) Chain: G
Molecule details ›
Chain: G
Length: 61 nucleotides
Theoretical weight: 18.76 KDa
DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3') Chain: L
Molecule details ›
Chain: L
Length: 30 nucleotides
Theoretical weight: 9.14 KDa
DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3') Chain: M
Molecule details ›
Chain: M
Length: 41 nucleotides
Theoretical weight: 12.66 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.06Å
Relevant EMDB volumes: EMD-20036
Expression system: Homo sapiens

Quick links

Citations

2 review citations

Structural insights into the evolution of the RAG recombinase.
Liu et al. (2022)
1 more

2 mentions without citation

Inner workings of RAG recombinase and its specialization for adaptive immunity.
Chen et al. (2021)
1 more