› 8opl

Electron Microscopy
2.41Å resolution

Virus-like Particle based on PVY coat protein with T43C and D136C mutation with helical architecture encapsidating ssRNA

Released:
DOI: 10.2210/pdb8opl/pdb
PDB entry 8opl coloured by chain, front view.
PDB entry 8opl coloured by chain, side view.
PDB entry 8opl coloured by chain, top view.
Source organism: Potato virus Y strain NTN
Primary publication:
From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y.
Kavčič L, Kežar A, Koritnik N, Žnidarič MT, Klobučar T, Vičič Ž, Merzel F, Holden E, Benesch JLP, Podobnik M
OpenAccess logo Commun Chem 7 14 (2024)
PMID: 38233506
Related structures: EMD-17072

Function and Biology Details

Reactions catalysed: 
Hydrolyzes glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln-|-(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved.
Hydrolyzes a Gly-|-Gly bond at its own C-terminus, commonly in the sequence -Tyr-Xaa-Val-Gly-|-Gly, in the processing of the potyviral polyprotein.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:

Structure analysis Details

Assembly composition:
hetero 54-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-239088 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Genome polyprotein (Fragment) Chains: Aa, Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, As, At, Au, Av, Aw, Ax, Ay, Az, Ba, Bk, Bl, Bm, Bn, Bo, Bp, Bq, Br, Bs
Molecule details ›
Chains: Aa, Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, As, At, Au, Av, Aw, Ax, Ay, Az, Ba, Bk, Bl, Bm, Bn, Bo, Bp, Bq, Br, Bs
Length: 267 amino acids
Theoretical weight: 29.93 KDa
Source organism: Potato virus Y strain NTN
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: C4N415 (Residues: 2795-3061; Coverage: 9%)
Sequence domains: Potyvirus coat protein
RNA (5'-R(P*UP*UP*UP*UP*U)-3') Chains: Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, Bb, Bc, Bd, Be, Bf, Bg, Bh, Bi, Bj, Bt, Bu, Bv, Bw, Bx, By, Bz, Ca, Cb
Molecule details ›
Chains: Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, Bb, Bc, Bd, Be, Bf, Bg, Bh, Bi, Bj, Bt, Bu, Bv, Bw, Bx, By, Bz, Ca, Cb
Length: 5 nucleotides
Theoretical weight: 1.49 KDa
Source organism: Potato virus Y strain NTN
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.41Å
Relevant EMDB volumes: EMD-17072
Expression system: Escherichia coli BL21(DE3)

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