› 6cg0

Electron Microscopy
3.17Å resolution

Cryo-EM structure of mouse RAG1/2 HFC complex (3.17 A)

Released:
DOI: 10.2210/pdb6cg0/pdb
PDB entry 6cg0 coloured by chain, front view.
PDB entry 6cg0 coloured by chain, side view.
PDB entry 6cg0 coloured by chain, top view.
Source organisms:
Primary publication:
Cracking the DNA Code for V(D)J Recombination.
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W
Mol Cell 70 358-370.e4 (2018)
PMID: 29628308
Related structures: EMD-7470

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 undecamer (preferred)
PDBe Complex ID:
PDB-CPX-119663 (preferred)
Entry contents:
3 distinct polypeptide molecules
6 distinct DNA molecules
Macromolecules (9 distinct):
V(D)J recombination-activating protein 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 775 amino acids
Theoretical weight: 88.52 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: P15919 (Residues: 265-1039; Coverage: 75%)
Gene name: Rag1
Sequence domains:
V(D)J recombination-activating protein 2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 520 amino acids
Theoretical weight: 58.16 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: P21784 (Residues: 1-520; Coverage: 99%)
Gene names: Rag-2, Rag2
Sequence domains:
High mobility group protein B1 Chain: N
Molecule details ›
Chain: N
Length: 126 amino acids
Theoretical weight: 14.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P09429 (Residues: 15-140; Coverage: 59%)
Gene names: HMG1, HMGB1
Sequence domains:
DNA (46-MER) Chain: F
Molecule details ›
Chain: F
Length: 46 nucleotides
Theoretical weight: 14.27 KDa
DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 16 nucleotides
Theoretical weight: 4.88 KDa
DNA (5'-D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') Chain: J
Molecule details ›
Chain: J
Length: 19 nucleotides
Theoretical weight: 5.8 KDa
DNA (60-MER) Chain: G
Molecule details ›
Chain: G
Length: 60 nucleotides
Theoretical weight: 18.48 KDa
DNA (30-MER) Chain: L
Molecule details ›
Chain: L
Length: 30 nucleotides
Theoretical weight: 9.14 KDa
DNA (41-MER) Chain: M
Molecule details ›
Chain: M
Length: 41 nucleotides
Theoretical weight: 12.66 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.17Å
Relevant EMDB volumes: EMD-7470
Expression systems:
  • Homo sapiens
  • Escherichia coli K-12

Quick links

Citations

14 review citations

RAG gene defects at the verge of immunodeficiency and immune dysregulation.
Villa et al. (2019)
13 more

4 mentions without citation

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