› 6w61

X-ray diffraction
2Å resolution

Crystal Structure of the methyltransferase-stimulatory factor complex of NSP16 and NSP10 from SARS CoV-2.

Released:
DOI: 10.2210/pdb6w61/pdb
PDB entry 6w61 coloured by chain, front view.
PDB entry 6w61 coloured by chain, side view.
PDB entry 6w61 coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Primary publication:
The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine
Rosas-Lemus M, Minasov G, Shuvalova L, Inniss NL, Kiryukhina O, Wiersum G, Kim Y, Jedrzejczak R, Maltseva NI, Endres M, Jaroszewski L, Godzik A, Joachimiak A, Satchell KJF
Biorxiv (2020)

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: 33.53 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: 140 amino acids
Theoretical weight: 14.93 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 4253-4392; Coverage: 2%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus RNA synthesis protein NSP10

Ligands and Environments


Cofactor: Ligand SAM 1 x SAM
3 bound ligands:
Ligand CL 1 x CL
Ligand EDO 3 x EDO
Ligand ZN 2 x ZN
1 modified residue:
Ligand KCX 1 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P3121
Unit cell:
a: 168.564Å b: 168.564Å c: 51.962Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.172 0.171 0.193
Expression system: Escherichia coli BL21(DE3)

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