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Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)

Electron Microscopy
3.9Å resolution
PDB entry 6cij coloured by chain, front view.
PDB entry 6cij coloured by chain, side view.
PDB entry 6cij coloured by chain, top view.
Source organisms:
Assembly composition:
hetero undecamer (preferred)
Entry contents: 3 distinct polypeptide molecules
6 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero undecamer
Accessible surface area: 115586.82 Å2
Buried surface area: 44141.76 Å2
Dissociation area: 1,515.71 Å2
Dissociation energy (ΔGdiss): 7.94 kcal/mol
Dissociation entropy (TΔSdiss): 13.71 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-119665

Macromolecules

V(D)J recombination-activating protein 1
Chains: A, C
Length: 776 amino acids
Theoretical weight: 88.67 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: P15919 (Residues: 265-1040; Coverage: 75%)
Gene name: Rag1
Pfam:
InterPro:
V(D)J recombination-activating protein 1 in PDB entry 6cij, assembly 1, front view.
V(D)J recombination-activating protein 1 in PDB entry 6cij, assembly 1, side view.
V(D)J recombination-activating protein 1 in PDB entry 6cij, assembly 1, top view.
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High mobility group protein B1
Chain: N
Length: 163 amino acids
Theoretical weight: 18.9 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P09429 (Residues: 1-163; Coverage: 76%)
Gene names: HMG1, HMGB1
Pfam:
InterPro:
High mobility group protein B1 in PDB entry 6cij, assembly 1, front view.
High mobility group protein B1 in PDB entry 6cij, assembly 1, side view.
High mobility group protein B1 in PDB entry 6cij, assembly 1, top view.
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V(D)J recombination-activating protein 2
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
Pfam:
InterPro:
V(D)J recombination-activating protein 2 in PDB entry 6cij, assembly 1, front view.
V(D)J recombination-activating protein 2 in PDB entry 6cij, assembly 1, side view.
V(D)J recombination-activating protein 2 in PDB entry 6cij, assembly 1, top view.
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DNA chain F
Name: DNA (46-MER)
Representative chains: F
Length: 46 nucleotides
Theoretical weight: 14.27 KDa
DNA (46-MER) in PDB entry 6cij, assembly 1, front view.
DNA (46-MER) in PDB entry 6cij, assembly 1, side view.
DNA (46-MER) in PDB entry 6cij, assembly 1, top view.
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DNA chain I
Name: DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
Representative chains: I
Length: 16 nucleotides
Theoretical weight: 4.88 KDa
DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') in PDB entry 6cij, assembly 1, front view.
DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') in PDB entry 6cij, assembly 1, side view.
DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') in PDB entry 6cij, assembly 1, top view.
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DNA chain J
Name: DNA (5'-D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
Representative chains: J
Length: 20 nucleotides
Theoretical weight: 6.09 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') in PDB entry 6cij, assembly 1, front view.
DNA (5'-D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') in PDB entry 6cij, assembly 1, side view.
DNA (5'-D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') in PDB entry 6cij, assembly 1, top view.
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DNA chain G
Name: DNA (60-MER)
Representative chains: G
Length: 61 nucleotides
Theoretical weight: 18.81 KDa
DNA (60-MER) in PDB entry 6cij, assembly 1, front view.
DNA (60-MER) in PDB entry 6cij, assembly 1, side view.
DNA (60-MER) in PDB entry 6cij, assembly 1, top view.
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DNA chain L
Name: DNA (30-MER)
Representative chains: L
Length: 30 nucleotides
Theoretical weight: 9.14 KDa
DNA (30-MER) in PDB entry 6cij, assembly 1, front view.
DNA (30-MER) in PDB entry 6cij, assembly 1, side view.
DNA (30-MER) in PDB entry 6cij, assembly 1, top view.
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DNA chain M
Name: DNA (41-MER)
Representative chains: M
Length: 41 nucleotides
Theoretical weight: 12.66 KDa
DNA (41-MER) in PDB entry 6cij, assembly 1, front view.
DNA (41-MER) in PDB entry 6cij, assembly 1, side view.
DNA (41-MER) in PDB entry 6cij, assembly 1, top view.
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