› 6w4b

X-ray diffraction
2.95Å resolution

The crystal structure of Nsp9 RNA binding protein of SARS CoV-2

Released:
DOI: 10.2210/pdb6w4b/pdb
PDB entry 6w4b coloured by chain, front view.
PDB entry 6w4b coloured by chain, side view.
PDB entry 6w4b coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Entry authors: Tan K, Kim Y, Jedrzejczak R, Maltseva N, Endres M, Michalska K, Joachimiak A, Center for Structural Genomics of Infectious Diseases (CSGID)

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145080 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Viral protein genome-linked nsp9 Chains: A, B
Molecule details ›
Chains: A, B
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli
UniProt:
  • Canonical: P0DTD1 (Residues: 4141-4253; Coverage: 2%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus replicase NSP9

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: P6122
Unit cell:
a: 89.883Å b: 89.883Å c: 132.587Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.242 0.24 0.276
Expression system: Escherichia coli

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