7l6t

X-ray diffraction
1.78Å resolution

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and two Magnesium (Mg) ions.

Released:

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-535733 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
2'-O-methyltransferase nsp16 Chain: A
Molecule details ›
Chain: A
Length: 300 amino acids
Theoretical weight: 33.56 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 6799-7096; Coverage: 4%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus 2'-O-methyltransferase
Non-structural protein 10 Chain: B
Molecule details ›
Chain: B
Length: 141 amino acids
Theoretical weight: 15 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 4254-4392; Coverage: 2%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus RNA synthesis protein NSP10
RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*UP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 7 nucleotides
Theoretical weight: 2.34 KDa

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P3121
Unit cell:
a: 169.351Å b: 169.351Å c: 52.629Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.142 0.141 0.162
Expression system: Escherichia coli BL21(DE3)