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Structure of Thermus thermophilus Argonaute bound to guide DNA and 15-mer target DNA

X-ray diffraction
2.248Å resolution
PDB entry 4n41 coloured by chain, front view.
PDB entry 4n41 coloured by chain, side view.
PDB entry 4n41 coloured by chain, top view.
Source organism: Thermus thermophilus
Assembly composition:
hetero trimer (preferred)
Entry contents: 1 distinct polypeptide molecule
3 distinct DNA molecules

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Assemblies

Assembly 1
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Assembly Name: Protein argonaute and DNA
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Multimeric state: hetero trimer
Accessible surface area: 31375.97 Å2
Buried surface area: 6713.17 Å2
Dissociation area: 1,595.53 Å2
Dissociation energy (ΔGdiss): 26.95 kcal/mol
Dissociation entropy (TΔSdiss): 10.8 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117863
Assembly 2 (preferred)
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Assembly Name: Protein argonaute and DNA
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Multimeric state: hetero trimer
Accessible surface area: 31615.0 Å2
Buried surface area: 7300.36 Å2
Dissociation area: 1,747.06 Å2
Dissociation energy (ΔGdiss): 34.01 kcal/mol
Dissociation entropy (TΔSdiss): 11 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-218974

Macromolecules

Protein argonaute
Chains: A, B
Length: 685 amino acids
Theoretical weight: 76.73 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q746M7 (Residues: 1-685; Coverage: 100%)
Gene names: TT_P0026, ago
Pfam:
InterPro:
CATH:
Protein argonaute in PDB entry 4n41, assembly 2, front view.
Protein argonaute in PDB entry 4n41, assembly 2, side view.
Protein argonaute in PDB entry 4n41, assembly 2, top view.
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DNA chains C, E
Name: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*T*GP*TP*AP*TP*AP*GP*T)-3'
Representative chains: C, E
Source organism: Thermus thermophilus [274]
Expression system: Not provided
Length: 21 nucleotides
Theoretical weight: 6.59 KDa
5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*T*GP*TP*AP*TP*AP*GP*T)-3' in PDB entry 4n41, assembly 2, front view.
5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*T*GP*TP*AP*TP*AP*GP*T)-3' in PDB entry 4n41, assembly 2, side view.
5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*T*GP*TP*AP*TP*AP*GP*T)-3' in PDB entry 4n41, assembly 2, top view.
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DNA chain D
Name: 5'-D(P*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
Representative chains: D
Source organism: Thermus thermophilus [274]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 3.87 KDa
5'-D(P*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3' in PDB entry 4n41, assembly 1, front view.
5'-D(P*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3' in PDB entry 4n41, assembly 1, side view.
5'-D(P*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3' in PDB entry 4n41, assembly 1, top view.
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DNA chain F
Name: 5'-D(*AP*AP*CP*CP*TP*AP*CP*TP*GP*CP*CP*TP*CP*G)-3'
Representative chains: F
Source organism: Thermus thermophilus [274]
Expression system: Not provided
Length: 14 nucleotides
Theoretical weight: 4.18 KDa
5'-D(*AP*AP*CP*CP*TP*AP*CP*TP*GP*CP*CP*TP*CP*G)-3' in PDB entry 4n41, assembly 2, front view.
5'-D(*AP*AP*CP*CP*TP*AP*CP*TP*GP*CP*CP*TP*CP*G)-3' in PDB entry 4n41, assembly 2, side view.
5'-D(*AP*AP*CP*CP*TP*AP*CP*TP*GP*CP*CP*TP*CP*G)-3' in PDB entry 4n41, assembly 2, top view.
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