› 8g6r

Electron Microscopy
3.3Å resolution

Porcine epidemic diarrhea virus core polymerase complex

Released:
DOI: 10.2210/pdb8g6r/pdb
PDB entry 8g6r coloured by chain, front view.
PDB entry 8g6r coloured by chain, side view.
PDB entry 8g6r coloured by chain, top view.
Source organism: Porcine epidemic diarrhea virus
Primary publication:
An alphacoronavirus polymerase structure reveals conserved co-factor functions.
Anderson TK, Hoferle PJ, Lee KW, Coon JJ, Kirchdoerfer RN
bioRxiv (2023)
PMID: 36993498
Related structures: EMD-29779

Function and Biology Details

Reactions catalysed: 
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]
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).
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-102513 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (5 distinct):
nsp12 Chain: A
Molecule details ›
Chain: A
Length: 921 amino acids
Theoretical weight: 104.94 KDa
Source organism: Porcine epidemic diarrhea virus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: A0A0U2C263 (Residues: 4103-5023; Coverage: 14%)
Sequence domains:
nsp8 Chain: B
Molecule details ›
Chain: B
Length: 114 amino acids
Theoretical weight: 12.56 KDa
Source organism: Porcine epidemic diarrhea virus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A1Z2R8Q6 (Residues: 3741-3854; Coverage: 2%)
Gene names: 1b, ORF1a
Sequence domains: Coronavirus replicase NSP8
nsp7 Chain: C
Molecule details ›
Chain: C
Length: 62 amino acids
Theoretical weight: 6.88 KDa
Source organism: Porcine epidemic diarrhea virus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0M4AW09 (Residues: 3581-3642; Coverage: 1%)
Gene name: ORF1
Sequence domains: Coronavirus replicase NSP7
RNA (5'-R(P*AP*AP*GP*AP*AP*GP*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 20 nucleotides
Theoretical weight: 6.41 KDa
RNA (5'-R(P*GP*GP*UP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*U)-3') Chain: J
Molecule details ›
Chain: J
Length: 20 nucleotides
Theoretical weight: 6.36 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-29779
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)

Quick links