› 3jbw

Electron Microscopy
4.6Å resolution

Cryo-electron microscopy structure of RAG Paired Complex (with NBD, no symmetry)

Released:
DOI: 10.2210/pdb3jbw/pdb
PDB entry 3jbw coloured by chain, front view.
PDB entry 3jbw coloured by chain, side view.
PDB entry 3jbw coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures.
Ru H, Chambers MG, Fu TM, Tong AB, Liao M, Wu H
Cell 163 1138-1152 (2015)
PMID: 26548953
Related structures: EMD-6489

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-116426 (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: 764 amino acids
Theoretical weight: 87.68 KDa
Source organism: Danio rerio
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O13033 (Residues: 271-1031; Coverage: 72%)
Gene name: 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:
12-RSS signal end forward strand Chain: E
Molecule details ›
Chain: E
Length: 34 nucleotides
Theoretical weight: 10.44 KDa
Nicked 12-RSS intermediate reverse strand Chain: F
Molecule details ›
Chain: F
Length: 50 nucleotides
Theoretical weight: 15.44 KDa
Nicked 23-RSS intermediate reverse strand Chain: G
Molecule details ›
Chain: G
Length: 61 nucleotides
Theoretical weight: 18.87 KDa
Nicked 23-RSS intermediate forward strand Chain: H
Molecule details ›
Chain: H
Length: 45 nucleotides
Theoretical weight: 13.81 KDa
5'-D(P*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3' Chains: I, J
Molecule details ›
Chains: I, J
Length: 16 nucleotides
Theoretical weight: 4.88 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.6Å
Relevant EMDB volumes: EMD-6489
Expression system: Spodoptera frugiperda

Quick links

Citations

18 review citations

Unravelling biological macromolecules with cryo-electron microscopy.
Fernandez-Leiro et al. (2016)
17 more

8 mentions without citation

Riches in RAGs: Revealing the V(D)J Recombinase through High-Resolution Structures.
Rodgers KK. (2017)
7 more