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SARS-CoV-2 RdRP catalytic complex with T33-1 RNA

Electron Microscopy
3Å resolution
PDB entry 7dte coloured by chain, front view.
PDB entry 7dte coloured by chain, side view.
PDB entry 7dte coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Assembly composition:
hetero hexamer (preferred)
Entry contents: 3 distinct polypeptide molecules
2 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: SARS-CoV-2 polymerase complex and RNA
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Multimeric state: hetero hexamer
Accessible surface area: 65712.94 Å2
Buried surface area: 19591.38 Å2
Dissociation area: 2,467.95 Å2
Dissociation energy (ΔGdiss): 37.45 kcal/mol
Dissociation entropy (TΔSdiss): 15.01 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-145055

Macromolecules

RNA-directed RNA polymerase nsp12
Chain: A
Length: 944 amino acids
Theoretical weight: 108.35 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 4393-5324; Coverage: 13%)
Gene names: 1a-1b, rep
Pfam:
InterPro:
RNA-directed RNA polymerase nsp12 in PDB entry 7dte, assembly 1, front view.
RNA-directed RNA polymerase nsp12 in PDB entry 7dte, assembly 1, side view.
RNA-directed RNA polymerase nsp12 in PDB entry 7dte, assembly 1, top view.
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Non-structural protein 8
Chains: B, D
Length: 200 amino acids
Theoretical weight: 22.06 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 3943-4140; Coverage: 3%)
Gene names: 1a-1b, rep
Pfam: Coronavirus replicase NSP8
InterPro:
Non-structural protein 8 in PDB entry 7dte, assembly 1, front view.
Non-structural protein 8 in PDB entry 7dte, assembly 1, side view.
Non-structural protein 8 in PDB entry 7dte, assembly 1, top view.
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Non-structural protein 7
Chain: C
Length: 85 amino acids
Theoretical weight: 9.4 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 3860-3942; Coverage: 1%)
Gene names: 1a-1b, rep
Pfam: Coronavirus replicase NSP7
InterPro:
Non-structural protein 7 in PDB entry 7dte, assembly 1, front view.
Non-structural protein 7 in PDB entry 7dte, assembly 1, side view.
Non-structural protein 7 in PDB entry 7dte, assembly 1, top view.
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RNA chain F
Name: RNA (57-MER)
Representative chains: F
Length: 57 nucleotides
Theoretical weight: 18.28 KDa
RNA (57-MER) in PDB entry 7dte, assembly 1, front view.
RNA (57-MER) in PDB entry 7dte, assembly 1, side view.
RNA (57-MER) in PDB entry 7dte, assembly 1, top view.
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RNA chain G
Name: RNA (33-MER)
Representative chains: G
Length: 34 nucleotides
Theoretical weight: 10.89 KDa
RNA (33-MER) in PDB entry 7dte, assembly 1, front view.
RNA (33-MER) in PDB entry 7dte, assembly 1, side view.
RNA (33-MER) in PDB entry 7dte, assembly 1, top view.
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