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Lambda excision HJ intermediate

Electron Microscopy
11Å resolution
PDB entry 5j0n coloured by chain, front view.
PDB entry 5j0n coloured by chain, side view.
PDB entry 5j0n coloured by chain, top view.
Source organisms:
Assembly composition:
hetero pentadecamer (preferred)
Entry contents: 4 distinct polypeptide molecules
4 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero pentadecamer
Accessible surface area: 166443.23 Å2
Buried surface area: 76654.03 Å2
Dissociation area: 2,803.85 Å2
Dissociation energy (ΔGdiss): -19.92 kcal/mol
Dissociation entropy (TΔSdiss): 33.66 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-118829

Macromolecules

Integrase
Chains: E, F, G, H
Length: 356 amino acids
Theoretical weight: 40.37 KDa
Source organism: Lambdavirus lambda
Expression system: Escherichia coli
UniProt:
  • Canonical: P03700 (Residues: 1-356; Coverage: 100%)
Gene name: int
Pfam:
InterPro:
Integrase in PDB entry 5j0n, assembly 1, front view.
Integrase in PDB entry 5j0n, assembly 1, side view.
Integrase in PDB entry 5j0n, assembly 1, top view.
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Integration host factor subunit alpha
Chains: I, K
Length: 96 amino acids
Theoretical weight: 11 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A6X7 (Residues: 2-97; Coverage: 97%)
Gene names: JW1702, b1712, hid, himA, ihfA
Pfam: Bacterial DNA-binding protein
InterPro:
Integration host factor subunit alpha in PDB entry 5j0n, assembly 1, front view.
Integration host factor subunit alpha in PDB entry 5j0n, assembly 1, side view.
Integration host factor subunit alpha in PDB entry 5j0n, assembly 1, top view.
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Integration host factor subunit beta
Chains: J, L
Length: 94 amino acids
Theoretical weight: 10.67 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A6Y1 (Residues: 1-94; Coverage: 100%)
Gene names: JW0895, b0912, himD, hip, ihfB
Pfam: Bacterial DNA-binding protein
InterPro:
Integration host factor subunit beta in PDB entry 5j0n, assembly 1, front view.
Integration host factor subunit beta in PDB entry 5j0n, assembly 1, side view.
Integration host factor subunit beta in PDB entry 5j0n, assembly 1, top view.
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Excisionase
Chains: M, N, O
Length: 55 amino acids
Theoretical weight: 6.79 KDa
Source organism: Lambdavirus lambda
Expression system: Escherichia coli
UniProt:
  • Canonical: P03699 (Residues: 1-55; Coverage: 76%)
Gene name: xis
Pfam: Excisionase-like protein
InterPro:
Excisionase in PDB entry 5j0n, assembly 1, front view.
Excisionase in PDB entry 5j0n, assembly 1, side view.
Excisionase in PDB entry 5j0n, assembly 1, top view.
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DNA chain A
Name: attP(-117 to +79)
Representative chains: A
Length: 197 nucleotides
Theoretical weight: 60.79 KDa
attP(-117 to +79) in PDB entry 5j0n, assembly 1, front view.
attP(-117 to +79) in PDB entry 5j0n, assembly 1, side view.
attP(-117 to +79) in PDB entry 5j0n, assembly 1, top view.
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DNA chain B
Name: attB(-21) to attP(+117)
Representative chains: B
Length: 139 nucleotides
Theoretical weight: 42.88 KDa
attB(-21) to attP(+117) in PDB entry 5j0n, assembly 1, front view.
attB(-21) to attP(+117) in PDB entry 5j0n, assembly 1, side view.
attB(-21) to attP(+117) in PDB entry 5j0n, assembly 1, top view.
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DNA chain C
Name: attB(-19 to +21)
Representative chains: C
Length: 41 nucleotides
Theoretical weight: 12.61 KDa
attB(-19 to +21) in PDB entry 5j0n, assembly 1, front view.
attB(-19 to +21) in PDB entry 5j0n, assembly 1, side view.
attB(-19 to +21) in PDB entry 5j0n, assembly 1, top view.
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DNA chain D
Name: attP(-79) to attB(+19)
Representative chains: D
Length: 99 nucleotides
Theoretical weight: 30.55 KDa
attP(-79) to attB(+19) in PDB entry 5j0n, assembly 1, front view.
attP(-79) to attB(+19) in PDB entry 5j0n, assembly 1, side view.
attP(-79) to attB(+19) in PDB entry 5j0n, assembly 1, top view.
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