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Structural basis for 5'-end-specific recognition of the guide RNA strand by the A. fulgidus PIWI protein

X-ray diffraction
2.5Å resolution
PDB entry 1ytu coloured by chain, front view.
PDB entry 1ytu coloured by chain, side view.
PDB entry 1ytu coloured by chain, top view.
Source organism: Archaeoglobus fulgidus DSM 4304
Assembly composition:
hetero trimer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Piwi protein and RNA
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Multimeric state: hetero trimer
Accessible surface area: 19251.97 Å2
Buried surface area: 2462.37 Å2
Dissociation area: 362.73 Å2
Dissociation energy (ΔGdiss): 0.44 kcal/mol
Dissociation entropy (TΔSdiss): 7.39 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-128085
Assembly 2
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Assembly Name: Piwi protein and RNA
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Multimeric state: hetero trimer
Accessible surface area: 20027.55 Å2
Buried surface area: 2652.38 Å2
Dissociation area: 418.57 Å2
Dissociation energy (ΔGdiss): 0.1 kcal/mol
Dissociation entropy (TΔSdiss): 7.39 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-128085

Macromolecules

Piwi protein
Chains: A, B
Length: 427 amino acids
Theoretical weight: 49.82 KDa
Source organism: Archaeoglobus fulgidus DSM 4304
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O28951 (Residues: 1-427; Coverage: 100%)
Gene name: AF_1318
Pfam: Piwi domain
InterPro:
CATH:
SCOP: PIWI domain
Piwi protein in PDB entry 1ytu, assembly 1, front view.
Piwi protein in PDB entry 1ytu, assembly 1, side view.
Piwi protein in PDB entry 1ytu, assembly 1, top view.
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RNA chains C, E
Name: 5'-R(P*AP*GP*AP*CP*AP*G)-3'
Representative chains: C, E
Source organism: Archaeoglobus fulgidus DSM 4304 [224325]
Expression system: Not provided
Length: 6 nucleotides
Theoretical weight: 1.94 KDa
5'-R(P*AP*GP*AP*CP*AP*G)-3' in PDB entry 1ytu, assembly 1, front view.
5'-R(P*AP*GP*AP*CP*AP*G)-3' in PDB entry 1ytu, assembly 1, side view.
5'-R(P*AP*GP*AP*CP*AP*G)-3' in PDB entry 1ytu, assembly 1, top view.
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RNA chains D, F
Name: 5'-R(P*UP*GP*UP*C)-3'
Representative chains: D, F
Source organism: Archaeoglobus fulgidus DSM 4304 [224325]
Expression system: Not provided
Length: 4 nucleotides
Theoretical weight: 1.22 KDa
5'-R(P*UP*GP*UP*C)-3' in PDB entry 1ytu, assembly 1, front view.
5'-R(P*UP*GP*UP*C)-3' in PDB entry 1ytu, assembly 1, side view.
5'-R(P*UP*GP*UP*C)-3' in PDB entry 1ytu, assembly 1, top view.
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