› 7dfh

Electron Microscopy
2.97Å resolution

Structure of COVID-19 RNA-dependent RNA polymerase bound to ribavirin

Released:
DOI: 10.2210/pdb7dfh/pdb
PDB entry 7dfh coloured by chain, front view.
PDB entry 7dfh coloured by chain, side view.
PDB entry 7dfh coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Entry authors: Li Z, Zhou Z, Yu X
Related structures: EMD-30664

Function and Biology Details

Reactions catalysed: 
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
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]
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
GTP + a 5'-diphospho-[mRNA] = diphosphate + a 5'-(5'-triphosphoguanosine)-[mRNA]
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).
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.
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-535719 (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: 943 amino acids
Theoretical weight: 107.97 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P0DTD1 (Residues: 4392-5324; Coverage: 13%)
Gene names: 1a-1b, rep
Sequence domains:
Non-structural protein 8 Chains: B, G
Molecule details ›
Chains: B, G
Length: 199 amino acids
Theoretical weight: 22.03 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P0DTD1 (Residues: 3942-4140; Coverage: 3%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus replicase NSP8
Non-structural protein 7 Chain: C
Molecule details ›
Chain: C
Length: 84 amino acids
Theoretical weight: 9.38 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P0DTD1 (Residues: 3859-3942; Coverage: 1%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus replicase NSP7
RNA (5'-R(P*GP*CP*UP*AP*UP*GP*UP*G*(LIG))-3') Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.54 KDa
RNA (5'-R(P*CP*CP*CP*CP*CP*AP*CP*AP*UP*AP*GP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.73 KDa

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 3 x MG
Ligand POP 2 x POP
Ligand RVP 1 x RVP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.97Å
Relevant EMDB volumes: EMD-30664
Expression system: Spodoptera frugiperda

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