› 8yb5

Electron Microscopy
4.2Å resolution

SARS-CoV-2 DMV nsp3-4 pore complex (consensus-pore, C6 symmetry)

Released:
DOI: 10.2210/pdb8yb5/pdb
PDB entry 8yb5 coloured by chain, front view.
PDB entry 8yb5 coloured by chain, side view.
PDB entry 8yb5 coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Entry authors: Huang YX, Zhong LJ, Zhang WX, Ni T
Related structures: EMD-39109

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 24-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-246040 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Papain-like protease nsp3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 1945 amino acids
Theoretical weight: 217.47 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTD1 (Residues: 819-2763; Coverage: 27%)
Gene names: 1a-1b, rep
Sequence domains:
Non-structural protein 4 Chains: C, D
Molecule details ›
Chains: C, D
Length: 500 amino acids
Theoretical weight: 56.23 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTD1 (Residues: 2764-3263; Coverage: 7%)
Gene names: 1a-1b, rep
Sequence domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.2Å
Relevant EMDB volumes: EMD-39109
Expression system: Homo sapiens

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