› 7lmc

X-ray diffraction
2.98Å resolution

Structure of SARS CoV-2 main protease shows simultaneous processing of its N- and C-terminii

Released:
DOI: 10.2210/pdb7lmc/pdb
PDB entry 7lmc coloured by chain, front view.
PDB entry 7lmc coloured by chain, side view.
PDB entry 7lmc coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Entry authors: Gajiwala KS, Ferre RA, Liu W, Ryan K

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145069 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Non-structural protein 4 Chains: E, F
Molecule details ›
Chains: E, F
Length: 6 amino acids
Theoretical weight: 618 Da
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli
UniProt:
  • Canonical: P0DTD1 (Residues: 3258-3263; Coverage: 0%)
Gene names: 1a-1b, rep
3C-like proteinase nsp5 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 306 amino acids
Theoretical weight: 33.79 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli
UniProt:
  • Canonical: P0DTD1 (Residues: 3264-3569; Coverage: 4%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus endopeptidase C30

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P1
Unit cell:
a: 62.77Å b: 66.3Å c: 80.26Å
α: 80.52° β: 89.46° γ: 70.55°
R-values:
R R work R free
0.212 0.208 0.288
Expression system: Escherichia coli

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