› 8h2i

Electron Microscopy
3.8Å resolution

Near-atomic structure of five-fold averaged PBCV-1 capsid

Released:
DOI: 10.2210/pdb8h2i/pdb
PDB entry 8h2i coloured by chain, front view.
PDB entry 8h2i coloured by chain, side view.
PDB entry 8h2i coloured by chain, top view.
Source organism: Paramecium bursaria Chlorella virus 1
Primary publication:
Near-atomic, non-icosahedrally averaged structure of giant virus Paramecium bursaria chlorella virus 1.
Shao Q, Agarkova IV, Noel EA, Dunigan DD, Liu Y, Wang A, Guo M, Xie L, Zhao X, Rossmann MG, Van Etten JL, Klose T, Fang Q
OpenAccess logo Nat Commun 13 6476 (2022)
PMID: 36309542
Related structures: EMD-34438

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 885-mer (preferred)
PDBe Complex ID:
PDB-CPX-125937 (preferred)
Entry contents:
26 distinct polypeptide molecules
Macromolecules (26 distinct):
Major capsid protein Chains: aA, aB, aC, aD, aE, aF, aG, aH, aI, aJ, aK, aL, aM, aN, aO, aP, aQ, aR, aS, aT, aU, aV, aW, aX, aY, aZ, aa, ab, ac, ad, ae, af, ag, ah, ai, aj, ak, al, am, an, ao, ap, aq, ar, as, at, au, av, aw, ax, ay, az, ba, bb, bc, bd, be, bf, bg, bh, bi, bj, bk, bl, bm, bn, bo, bp, bq, br, bs, bt
Molecule details ›
Chains: aA, aB, aC, aD, aE, aF, aG, aH, aI, aJ, aK, aL, aM, aN, aO, aP, aQ, aR, aS, aT, aU, aV, aW, aX, aY, aZ, aa, ab, ac, ad, ae, af, ag, ah, ai, aj, ak, al, am, an, ao, ap, aq, ar, as, at, au, av, aw, ax, ay, az, ba, bb, bc, bd, be, bf, bg, bh, bi, bj, bk, bl, bm, bn, bo, bp, bq, br, bs, bt
Length: 437 amino acids
Theoretical weight: 48.2 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: P30328 (Residues: 1-437; Coverage: 100%)
Gene name: A430L
Sequence domains:
Capsid protein Chains: bA, bB, bu, bv, bw, bx, by, bz
Molecule details ›
Chains: bA, bB, bu, bv, bw, bx, by, bz
Length: 520 amino acids
Theoretical weight: 58.14 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: O41104 (Residues: 1-520; Coverage: 100%)
Gene name: A622L
Sequence domains:
Major capsid protein VP54 Chain: bC
Molecule details ›
Chain: bC
Length: 486 amino acids
Theoretical weight: 55.73 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: M1I493 (Residues: 1-486; Coverage: 100%)
Gene names: NE-JV-4_430R, PBCVNEJV4_430R
Sequence domains:
Capsid protein Chains: bD, bF, cX, cZ, dd, df, dj, dk, dl, dp, dr
Molecule details ›
Chains: bD, bF, cX, cZ, dd, df, dj, dk, dl, dp, dr
Length: 403 amino acids
Theoretical weight: 45.12 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q89346 (Residues: 1-403; Coverage: 100%)
Gene name: A011L
Sequence domains:
Capsid protein Chains: bE, cY, de, dq
Molecule details ›
Chains: bE, cY, de, dq
Length: 401 amino acids
Theoretical weight: 45.03 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q89345 (Residues: 1-401; Coverage: 100%)
Gene name: A010R
Sequence domains:
DUF5901 domain-containing protein Chain: bG
Molecule details ›
Chain: bG
Length: 530 amino acids
Theoretical weight: 57.56 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: M1I677 (Residues: 1-530; Coverage: 100%)
Gene names: IL-3A_593R, PBCVIL3A_593R
Sequence domains: Family of unknown function (DUF5901)
Minor capsid protein P2 Chain: bH
Molecule details ›
Chain: bH
Length: 576 amino acids
Theoretical weight: 63.89 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q84656 (Residues: 1-576; Coverage: 100%)
Gene name: A342L
Sequence domains: Family of unknown function (DUF5899)
Minor capsid protein 3 Chains: bI, bJ, bK
Molecule details ›
Chains: bI, bJ, bK
Length: 171 amino acids
Theoretical weight: 19.12 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q98573 (Residues: 1-171; Coverage: 100%)
Gene name: A523R
Minor capsid protein P4 Chains: bL, bM, bN, bO
Molecule details ›
Chains: bL, bM, bN, bO
Length: 181 amino acids
Theoretical weight: 20.64 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: O41054 (Residues: 1-181; Coverage: 100%)
Gene name: A572R
Minor capsid protein P5 Chain: bP
Molecule details ›
Chain: bP
Length: 146 amino acids
Theoretical weight: 16.46 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q98576 (Residues: 1-146; Coverage: 100%)
Gene name: A526R
Minor capsid protein P6 Chain: bQ
Molecule details ›
Chain: bQ
Length: 216 amino acids
Theoretical weight: 24.04 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q84523 (Residues: 1-216; Coverage: 100%)
Gene name: A203R
Minor capsid protein P8 Chain: bR
Molecule details ›
Chain: bR
Length: 173 amino acids
Theoretical weight: 19.23 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: O41126 (Residues: 1-173; Coverage: 100%)
Gene name: A644R
Sequence domains: Family of unknown function (DUF5761)
Minor capsid protein P9 Chain: bS
Molecule details ›
Chain: bS
Length: 210 amino acids
Theoretical weight: 23.41 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q98459 (Residues: 1-210; Coverage: 100%)
Gene name: A407L
Sequence domains: Family of unknown function (DUF5762)
Minor capsid protein P11 Chains: bT, bU, bV, bW, bX, bY, bZ, ca, cb, cc, cd, ce
Molecule details ›
Chains: bT, bU, bV, bW, bX, bY, bZ, ca, cb, cc, cd, ce
Length: 207 amino acids
Theoretical weight: 23.32 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q84666 (Residues: 1-207; Coverage: 100%)
Gene name: A352L
Minor capsid protein P12 Chain: cf
Molecule details ›
Chain: cf
Length: 151 amino acids
Theoretical weight: 17.72 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q84459 (Residues: 1-151; Coverage: 100%)
Gene name: A139L
Minor capsid protein P13 Chain: cg
Molecule details ›
Chain: cg
Length: 98 amino acids
Theoretical weight: 11.07 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q98473 (Residues: 1-98; Coverage: 100%)
Gene name: A421R
P15 Chain: ch
Molecule details ›
Chain: ch
Length: 155 amino acids
Theoretical weight: 18.63 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q98534 (Residues: 1-155; Coverage: 100%)
Gene name: A484L
P16 Chain: ci
Molecule details ›
Chain: ci
Length: 93 amino acids
Theoretical weight: 9.84 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q98530 (Residues: 1-93; Coverage: 100%)
Gene name: A480L
P17 Chains: cj, ck, cl, cm
Molecule details ›
Chains: cj, ck, cl, cm
Length: 80 amino acids
Theoretical weight: 9.12 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q84629 (Residues: 1-80; Coverage: 100%)
Gene name: A314R
P18 Chains: cn, co
Molecule details ›
Chains: cn, co
Length: 148 amino acids
Theoretical weight: 16.5 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q84533 (Residues: 1-148; Coverage: 100%)
Gene name: A213L
Capsid protein Chains: cA, cB, cC, cD, cE, cF, cG, cH, cI, cJ, cK, cL, cM, cN, cp, cq, cr, cs, ct, cu, cv, cw, cx, cy, cz
Molecule details ›
Chains: cA, cB, cC, cD, cE, cF, cG, cH, cI, cJ, cK, cL, cM, cN, cp, cq, cr, cs, ct, cu, cv, cw, cx, cy, cz
Length: 378 amino acids
Theoretical weight: 43.09 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q84602 (Residues: 1-378; Coverage: 100%)
Gene name: A286R
Chlorovirus glycoprotein repeat domain-containing protein Chains: cO, cQ, da, dc, dg, di, ds, du
Molecule details ›
Chains: cO, cQ, da, dc, dg, di, ds, du
Length: 1335 amino acids
Theoretical weight: 137.67 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q89353 (Residues: 1-1335; Coverage: 100%)
Gene name: A018L
Sequence domains: Chlorovirus glycoprotein repeat
Chlorovirus glycoprotein repeat domain-containing protein Chains: cP, db, dh, dt
Molecule details ›
Chains: cP, db, dh, dt
Length: 1369 amino acids
Theoretical weight: 141.41 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q89349 (Residues: 1-1369; Coverage: 100%)
Gene name: A014R
Capsid protein Chains: cR, cS, cT
Molecule details ›
Chains: cR, cS, cT
Length: 400 amino acids
Theoretical weight: 45.59 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: O41040 (Residues: 1-400; Coverage: 100%)
Gene name: A558L
Sequence domains:
Peptidase G2 IMC autoproteolytic cleavage domain-containing protein Chains: cU, cV, cW
Molecule details ›
Chains: cU, cV, cW
Length: 1343 amino acids
Theoretical weight: 137.93 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q84443 (Residues: 1-1343; Coverage: 100%)
Gene name: A122/123R
Sequence domains:
Chlorovirus glycoprotein repeat domain-containing protein Chains: dm, dn, do
Molecule details ›
Chains: dm, dn, do
Length: 1359 amino acids
Theoretical weight: 140.12 KDa
Source organism: Paramecium bursaria Chlorella virus 1
UniProt:
  • Canonical: Q89360 (Residues: 1-1359; Coverage: 100%)
Gene name: A025/027/029L

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-34438

Quick links

Citations

4 review citations

Kratosvirus quantuckense: the history and novelty of an algal bloom disrupting virus and a model for giant virus research.
Truchon et al. (2023)
3 more