› 5w8u

X-ray diffraction
2.41Å resolution

Crystal structure of MERS-CoV papain-like protease in complex with the C-terminal domain of human ISG15

Released:
DOI: 10.2210/pdb5w8u/pdb
PDB entry 5w8u coloured by chain, front view.
PDB entry 5w8u coloured by chain, side view.
PDB entry 5w8u coloured by chain, top view.
Source organisms:
Primary publication:
Structurally Guided Removal of DeISGylase Biochemical Activity from Papain-Like Protease Originating from Middle East Respiratory Syndrome Coronavirus.
Daczkowski CM, Goodwin OY, Dzimianski JV, Farhat JJ, Pegan SD
J Virol 91 (2017)
PMID: 28931677

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126023 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
ORF1ab protein Chains: A, C
Molecule details ›
Chains: A, C
Length: 322 amino acids
Theoretical weight: 35.82 KDa
Source organism: Human betacoronavirus 2c EMC/2012
Expression system: Escherichia coli
UniProt:
  • Canonical: M4STU1 (Residues: 1482-1803; Coverage: 5%)
Gene name: ORF1ab
Sequence domains: Coronavirus papain-like peptidase
Structure domains:
Ubiquitin-like protein ISG15 Chains: B, D
Molecule details ›
Chains: B, D
Length: 79 amino acids
Theoretical weight: 8.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P05161 (Residues: 80-156; Coverage: 47%)
Gene names: G1P2, ISG15, UCRP
Sequence domains: Ubiquitin family

Ligands and Environments

3 bound ligands:
Ligand ZN 6 x ZN
Ligand AYE 2 x AYE
Ligand MPD 8 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P43
Unit cell:
a: 86.37Å b: 86.37Å c: 224.087Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.212 0.237
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein.
Lei et al. (2018)
3 more

8 mentions without citation

Coronaviral PLpro proteases and the immunomodulatory roles of conjugated versus free Interferon Stimulated Gene product-15 (ISG15).
Gold et al. (2022)
7 more