7c2k

Electron Microscopy
2.93Å resolution

COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex

Released:

Function and Biology Details

Reactions catalysed:
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
ATP + H(2)O = ADP + phosphate
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (5 distinct):
RNA-directed RNA polymerase nsp12 Chain: A
Molecule details ›
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
Sequence domains:
Non-structural protein 8 Chains: B, D
Molecule details ›
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
Sequence domains: Coronavirus replicase NSP8
Non-structural protein 7 Chain: C
Molecule details ›
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
Sequence domains: Coronavirus replicase NSP7
RNA (29-MER) Chain: F
Molecule details ›
Chain: F
Length: 29 nucleotides
Theoretical weight: 9.29 KDa
RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*CP*AP*CP*AP*GP*G*(F86)P*G)-3') Chain: G
Molecule details ›
Chain: G
Length: 18 nucleotides
Theoretical weight: 5.84 KDa

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.93Å
Relevant EMDB volumes: EMD-30275
Expression system: Escherichia coli BL21(DE3)