› 7r1t

X-ray diffraction
2.7Å resolution

Crystal structure of SARS-CoV-2 nsp10/nsp16 in complex with the SS148 inhibitor

Released:
DOI: 10.2210/pdb7r1t/pdb
PDB entry 7r1t coloured by chain, front view.
PDB entry 7r1t coloured by chain, side view.
PDB entry 7r1t coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Primary publication:
Crystal structure of SARS-CoV-2 nsp10-nsp16 in complex with small molecule inhibitors, SS148 and WZ16.
Klima M, Khalili Yazdi A, Li F, Chau I, Hajian T, Bolotokova A, Kaniskan HÜ, Han Y, Wang K, Li D, Luo M, Jin J, Boura E, Vedadi M
Protein Sci 31 e4395 (2022)
PMID: 36040262

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145023 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
2'-O-methyltransferase nsp16 Chain: A
Molecule details ›
Chain: A
Length: 299 amino acids
Theoretical weight: 33.49 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 6798-7096; Coverage: 4%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus 2'-O-methyltransferase
Non-structural protein 10 Chain: B
Molecule details ›
Chain: B
Length: 123 amino acids
Theoretical weight: 13.13 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 4263-4384; Coverage: 2%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus RNA synthesis protein NSP10

Ligands and Environments


Cofactor: Ligand 6NR 1 x 6NR
3 bound ligands:
Ligand PO4 2 x PO4
Ligand MES 1 x MES
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P3121
Unit cell:
a: 168.216Å b: 168.216Å c: 51.505Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.207 0.205 0.247
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Coronavirus 2'-O-methyltransferase: A promising therapeutic target.
Schindewolf et al. (2023)
1 more

2 mentions without citation

Crystal structure of SARS-CoV-2 nsp10-nsp16 in complex with small molecule inhibitors, SS148 and WZ16.
Klima et al. (2022)
1 more