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Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-mer siRNA having 5'-p and UU-3' ends (1.95 Angstrom resolution)

X-ray diffraction
1.958Å resolution
PDB entry 4ngd coloured by chain, front view.
PDB entry 4ngd coloured by chain, side view.
PDB entry 4ngd coloured by chain, top view.
Source organism: Homo sapiens
Assemblies composition:
hetero trimer (preferred)
hetero tetramer
Entry contents: 1 distinct polypeptide molecule
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Endoribonuclease Dicer and RNA
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Multimeric state: hetero trimer
Accessible surface area: 18911.55 Å2
Buried surface area: 3486.3 Å2
Dissociation area: 664.19 Å2
Dissociation energy (ΔGdiss): -3.63 kcal/mol
Dissociation entropy (TΔSdiss): 10.34 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-219673
Assembly 2
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Assembly Name: Endoribonuclease Dicer and RNA
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Multimeric state: hetero tetramer
Accessible surface area: 32725.61 Å2
Buried surface area: 6023.98 Å2
Dissociation area: 853.49 Å2
Dissociation energy (ΔGdiss): -5.6 kcal/mol
Dissociation entropy (TΔSdiss): 13.9 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-194049

Macromolecules

Endoribonuclease Dicer
Chain: A
Length: 302 amino acids
Theoretical weight: 34.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UPY3 (Residues: 765-1065; Coverage: 16%)
Gene names: DICER, DICER1, HERNA, KIAA0928
Pfam:
InterPro:
CATH: paz domain
Endoribonuclease Dicer in PDB entry 4ngd, assembly 1, front view.
Endoribonuclease Dicer in PDB entry 4ngd, assembly 1, side view.
Endoribonuclease Dicer in PDB entry 4ngd, assembly 1, top view.
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RNA chain B
Name: 5'-R(P*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'
Representative chains: B
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 12 nucleotides
Theoretical weight: 3.79 KDa
5'-R(P*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3' in PDB entry 4ngd, assembly 1, front view.
5'-R(P*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3' in PDB entry 4ngd, assembly 1, side view.
5'-R(P*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3' in PDB entry 4ngd, assembly 1, top view.
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