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Structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B2)

Electron Microscopy
4.1Å resolution
PDB entry 6kut coloured by chain, front view.
PDB entry 6kut coloured by chain, side view.
PDB entry 6kut coloured by chain, top view.
Source organism: Influenza D virus (D/swine/Oklahoma/1334/2011)
Assembly composition:
hetero pentamer (preferred)
Entry contents: 3 distinct polypeptide molecules
2 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero pentamer
Accessible surface area: 76999.93 Å2
Buried surface area: 37394.69 Å2
Dissociation area: 1,363.19 Å2
Dissociation energy (ΔGdiss): 12.51 kcal/mol
Dissociation entropy (TΔSdiss): 10.9 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-125653

Macromolecules

Polymerase 3
Chain: A
Length: 710 amino acids
Theoretical weight: 83.04 KDa
Source organism: Influenza D virus (D/swine/Oklahoma/1334/2011)
Expression system: Spodoptera aff. frugiperda 1 BOLD-2017
UniProt:
  • Canonical: K9LHJ4 (Residues: 1-710; Coverage: 100%)
Gene name: P3
Pfam: Influenza RNA-dependent RNA polymerase subunit PA
InterPro:
Polymerase 3 in PDB entry 6kut, assembly 1, front view.
Polymerase 3 in PDB entry 6kut, assembly 1, side view.
Polymerase 3 in PDB entry 6kut, assembly 1, top view.
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RNA-directed RNA polymerase catalytic subunit
Chain: B
Length: 753 amino acids
Theoretical weight: 86.14 KDa
Source organism: Influenza D virus (D/swine/Oklahoma/1334/2011)
Expression system: Spodoptera aff. frugiperda 1 BOLD-2017
UniProt:
  • Canonical: K9LH03 (Residues: 1-753; Coverage: 100%)
Gene name: PB1
Pfam:
InterPro:
RNA-directed RNA polymerase catalytic subunit in PDB entry 6kut, assembly 1, front view.
RNA-directed RNA polymerase catalytic subunit in PDB entry 6kut, assembly 1, side view.
RNA-directed RNA polymerase catalytic subunit in PDB entry 6kut, assembly 1, top view.
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Polymerase basic protein 2
Chain: C
Length: 772 amino acids
Theoretical weight: 88.48 KDa
Source organism: Influenza D virus (D/swine/Oklahoma/1334/2011)
Expression system: Spodoptera aff. frugiperda 1 BOLD-2017
UniProt:
  • Canonical: K9LHF3 (Residues: 1-772; Coverage: 100%)
Gene name: PB2
Pfam:
InterPro: Influenza RNA-dependent RNA polymerase subunit PB2
Polymerase basic protein 2 in PDB entry 6kut, assembly 1, front view.
Polymerase basic protein 2 in PDB entry 6kut, assembly 1, side view.
Polymerase basic protein 2 in PDB entry 6kut, assembly 1, top view.
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RNA chain R
Name: 3'-vRNA
Representative chains: R
Length: 14 nucleotides
Theoretical weight: 4.34 KDa
3'-vRNA in PDB entry 6kut, assembly 1, front view.
3'-vRNA in PDB entry 6kut, assembly 1, side view.
3'-vRNA in PDB entry 6kut, assembly 1, top view.
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RNA chain V
Name: 5'-vRNA
Representative chains: V
Length: 15 nucleotides
Theoretical weight: 4.92 KDa
5'-vRNA in PDB entry 6kut, assembly 1, front view.
5'-vRNA in PDB entry 6kut, assembly 1, side view.
5'-vRNA in PDB entry 6kut, assembly 1, top view.
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