› 8opc

Electron Microscopy
2.99Å resolution

Virus-like Particle based on PVY coat protein with helical architecture encapsidating ssRNA

Released:
DOI: 10.2210/pdb8opc/pdb
PDB entry 8opc coloured by chain, front view.
PDB entry 8opc coloured by chain, side view.
PDB entry 8opc 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-17048

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 56-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-239011 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Coat protein Chains: Aa, Ac, Ae, Ag, Ai, Ak, Am, Ao, Aq, As, Au, Aw, Ay, Ba, Bc, Be, Bg, Bi, Bk, Bm, Bo, Bq, Bs, Bu, Bw, By, Ca, Cc
Molecule details ›
Chains: Aa, Ac, Ae, Ag, Ai, Ak, Am, Ao, Aq, As, Au, Aw, Ay, Ba, Bc, Be, Bg, Bi, Bk, Bm, Bo, Bq, Bs, Bu, Bw, By, Ca, Cc
Length: 267 amino acids
Theoretical weight: 29.94 KDa
Source organism: Potato virus Y strain NTN
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0A7DIV0 (Residues: 1-267; Coverage: 100%)
Sequence domains: Potyvirus coat protein
RNA (5'-R(P*UP*UP*UP*UP*U)-3') Chains: Ab, Ad, Af, Ah, Aj, Al, An, Ap, Ar, At, Av, Ax, Az, Bb, Bd, Bf, Bh, Bj, Bl, Bn, Bp, Br, Bt, Bv, Bx, Bz, Cb, Cd
Molecule details ›
Chains: Ab, Ad, Af, Ah, Aj, Al, An, Ap, Ar, At, Av, Ax, Az, Bb, Bd, Bf, Bh, Bj, Bl, Bn, Bp, Br, Bt, Bv, Bx, Bz, Cb, Cd
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: 2.99Å
Relevant EMDB volumes: EMD-17048
Expression system: Escherichia coli BL21(DE3)

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