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Cryo-EM structure of RAG in complex with one melted RSS and one unmelted RSS

Electron Microscopy
4Å resolution
PDB entry 6dbr coloured by chain, front view.
PDB entry 6dbr coloured by chain, side view.
PDB entry 6dbr coloured by chain, top view.
Source organisms:
Assembly composition:
hetero octamer (preferred)
Entry contents: 2 distinct polypeptide molecules
4 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 octamer
Accessible surface area: 90059.22 Å2
Buried surface area: 26178.65 Å2
Dissociation area: 3,101.02 Å2
Dissociation energy (ΔGdiss): 41.21 kcal/mol
Dissociation entropy (TΔSdiss): 16.67 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-238532

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 6dbr, assembly 1, front view.
Maltose/maltodextrin-binding periplasmic protein in PDB entry 6dbr, assembly 1, side view.
Maltose/maltodextrin-binding periplasmic protein in PDB entry 6dbr, 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 6dbr, assembly 1, front view.
V(D)J recombination-activating protein 2 in PDB entry 6dbr, assembly 1, side view.
V(D)J recombination-activating protein 2 in PDB entry 6dbr, assembly 1, top view.
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DNA chain E
Name: Forward strand of unmelted RSS substrate DNA
Representative chains: E
Length: 34 nucleotides
Theoretical weight: 10.45 KDa
Forward strand of unmelted RSS substrate DNA in PDB entry 6dbr, assembly 1, front view.
Forward strand of unmelted RSS substrate DNA in PDB entry 6dbr, assembly 1, side view.
Forward strand of unmelted RSS substrate DNA in PDB entry 6dbr, assembly 1, top view.
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DNA chain F
Name: Reverse strand of unmelted RSS substrate DNA
Representative chains: F
Length: 34 nucleotides
Theoretical weight: 10.47 KDa
Reverse strand of unmelted RSS substrate DNA in PDB entry 6dbr, assembly 1, front view.
Reverse strand of unmelted RSS substrate DNA in PDB entry 6dbr, assembly 1, side view.
Reverse strand of unmelted RSS substrate DNA in PDB entry 6dbr, assembly 1, top view.
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DNA chain G
Name: Forward strand of melted RSS substrate DNA
Representative chains: G
Length: 34 nucleotides
Theoretical weight: 10.43 KDa
Forward strand of melted RSS substrate DNA in PDB entry 6dbr, assembly 1, front view.
Forward strand of melted RSS substrate DNA in PDB entry 6dbr, assembly 1, side view.
Forward strand of melted RSS substrate DNA in PDB entry 6dbr, assembly 1, top view.
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DNA chain H
Name: Reverse strand of melted RSS substrate DNA
Representative chains: H
Length: 34 nucleotides
Theoretical weight: 10.49 KDa
Reverse strand of melted RSS substrate DNA in PDB entry 6dbr, assembly 1, front view.
Reverse strand of melted RSS substrate DNA in PDB entry 6dbr, assembly 1, side view.
Reverse strand of melted RSS substrate DNA in PDB entry 6dbr, assembly 1, top view.
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