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

Electron Microscopy
4.7Å resolution
PDB entry 6dbw coloured by chain, front view.
PDB entry 6dbw coloured by chain, side view.
PDB entry 6dbw coloured by chain, top view.
Source organisms:
Assembly composition:
hetero hexamer (preferred)
Entry contents: 2 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: V(D)J recombination-activating protein 2 and Maltose/maltodextrin-binding periplasmic protein, V(D)J recombination-activating protein 1 and DNA
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Multimeric state: hetero hexamer
Accessible surface area: 98714.09 Å2
Buried surface area: 25965.53 Å2
Dissociation area: 1,801.86 Å2
Dissociation energy (ΔGdiss): 4.91 kcal/mol
Dissociation entropy (TΔSdiss): 14.9 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-119729

Macromolecules

Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
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%)
    • nullnull
Gene names: JW3994, b4034, malE, rag1
Pfam:
InterPro:
Maltose/maltodextrin-binding periplasmic protein in PDB entry 6dbw, assembly 1, front view.
Maltose/maltodextrin-binding periplasmic protein in PDB entry 6dbw, assembly 1, side view.
Maltose/maltodextrin-binding periplasmic protein in PDB entry 6dbw, assembly 1, top view.
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V(D)J recombination-activating protein 2
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
Pfam:
InterPro:
V(D)J recombination-activating protein 2 in PDB entry 6dbw, assembly 1, front view.
V(D)J recombination-activating protein 2 in PDB entry 6dbw, assembly 1, side view.
V(D)J recombination-activating protein 2 in PDB entry 6dbw, assembly 1, top view.
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DNA chain E
Name: Forward strand of 12-RSS substrate DNA
Representative chains: E
Length: 50 nucleotides
Theoretical weight: 15.36 KDa
Forward strand of 12-RSS substrate DNA in PDB entry 6dbw, assembly 1, front view.
Forward strand of 12-RSS substrate DNA in PDB entry 6dbw, assembly 1, side view.
Forward strand of 12-RSS substrate DNA in PDB entry 6dbw, assembly 1, top view.
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DNA chain F
Name: Reverse strand of 12-RSS substrate DNA
Representative chains: F
Length: 50 nucleotides
Theoretical weight: 15.44 KDa
Reverse strand of 12-RSS substrate DNA in PDB entry 6dbw, assembly 1, front view.
Reverse strand of 12-RSS substrate DNA in PDB entry 6dbw, assembly 1, side view.
Reverse strand of 12-RSS substrate DNA in PDB entry 6dbw, assembly 1, top view.
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