6NCL image
Deposition Date 2018-12-11
Release Date 2019-01-30
Last Version Date 2024-10-16
Entry Detail
PDB ID:
6NCL
Keywords:
Title:
Near-atomic structure of icosahedrally averaged PBCV-1 capsid
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:P14
Gene (Uniprot):A500L
Chain IDs:A (auth: a0)
Chain Length:352
Number of Molecules:1
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P9
Gene (Uniprot):A407L
Chain IDs:B (auth: a1)
Chain Length:210
Number of Molecules:1
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P10
Gene (Uniprot):A454L
Chain IDs:C (auth: a2), D (auth: a3)
Chain Length:289
Number of Molecules:2
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P7
Gene (Uniprot):A262/263L
Chain IDs:E (auth: a4)
Chain Length:256
Number of Molecules:1
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P6
Gene (Uniprot):A203R
Chain IDs:F (auth: a5)
Chain Length:216
Number of Molecules:1
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P1
Gene (Uniprot):A310L
Chain IDs:G (auth: a6)
Chain Length:170
Number of Molecules:1
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P12
Gene (Uniprot):A139L
Chain IDs:H (auth: a7)
Chain Length:151
Number of Molecules:1
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P5
Gene (Uniprot):A526R
Chain IDs:I (auth: a8)
Chain Length:146
Number of Molecules:1
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P11
Gene (Uniprot):A352L
Chain IDs:J (auth: a9), K (auth: b0), L (auth: b1), M (auth: b2), N (auth: b3), O (auth: b4), P (auth: b5), R (auth: b7), S (auth: b8), T (auth: c0), U (auth: c1), KD (auth: l5)
Chain Length:207
Number of Molecules:12
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P2
Gene (Uniprot):A342L
Chain IDs:Q (auth: b6)
Chain Length:576
Number of Molecules:1
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P4
Gene (Uniprot):A572R
Chain IDs:V (auth: c2), W (auth: c3), X (auth: c4), Y (auth: c5)
Chain Length:181
Number of Molecules:4
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P3
Gene (Uniprot):A523R
Chain IDs:Z (auth: c6), AA (auth: c7), BA (auth: c8)
Chain Length:171
Number of Molecules:3
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P8
Gene (Uniprot):A644R
Chain IDs:CA (auth: c9)
Chain Length:173
Number of Molecules:1
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:Major capsid protein
Gene (Uniprot):A430L
Chain IDs:DA (auth: d0), EA (auth: d1), FA (auth: d2), GA (auth: d3), HA (auth: d4), IA (auth: d5), JA (auth: d6), KA (auth: d7), LA (auth: d8), MA (auth: d9), NA (auth: e0), OA (auth: e1), PA (auth: e2), QA (auth: e3), RA (auth: e4), SA (auth: e5), TA (auth: e6), UA (auth: e7), VA (auth: e8), WA (auth: e9), XA (auth: f0), YA (auth: f1), ZA (auth: f2), AB (auth: f3), BB (auth: f4), CB (auth: f5), DB (auth: f6), EB (auth: f7), FB (auth: f8), GB (auth: f9), HB (auth: g0), IB (auth: g1), JB (auth: g2), KB (auth: g3), LB (auth: g4), MB (auth: g5), NB (auth: g6), OB (auth: g7), PB (auth: g8), QB (auth: g9), RB (auth: h0), SB (auth: h1), TB (auth: h2), UB (auth: h3), VB (auth: h4), WB (auth: h5), XB (auth: h6), YB (auth: h7), ZB (auth: h8), AC (auth: h9), BC (auth: i0), CC (auth: i1), DC (auth: i2), EC (auth: i3), FC (auth: i4), GC (auth: i5), HC (auth: i6), IC (auth: i7), JC (auth: i8), KC (auth: i9), LC (auth: j0), MC (auth: j1), NC (auth: j2), OC (auth: j3), PC (auth: j4), QC (auth: j5), RC (auth: j6), SC (auth: j7), TC (auth: j8), UC (auth: j9), VC (auth: k0), WC (auth: k1), XC (auth: k2), YC (auth: k3), ZC (auth: k4), AD (auth: k5), BD (auth: k6), CD (auth: k7), DD (auth: k8), ED (auth: k9), FD (auth: l0), GD (auth: l1), HD (auth: l2), ID (auth: l3)
Chain Length:437
Number of Molecules:84
Biological Source:Paramecium bursaria Chlorella virus 1
Polymer Type:polypeptide(L)
Molecule:P13
Gene (Uniprot):A421R
Chain IDs:JD (auth: l4)
Chain Length:98
Number of Molecules:1
Biological Source:Paramecium bursaria Chlorella virus 1
Ligand Molecules
Primary Citation
Near-atomic structure of a giant virus.
Nat Commun 10 388 388 (2019)
PMID: 30674888 DOI: 10.1038/s41467-019-08319-6

Abstact

Although the nucleocytoplasmic large DNA viruses (NCLDVs) are one of the largest group of viruses that infect many eukaryotic hosts, the near-atomic resolution structures of these viruses have remained unknown. Here we describe a 3.5 Å resolution icosahedrally averaged capsid structure of Paramecium bursaria chlorella virus 1 (PBCV-1). This structure consists of 5040 copies of the major capsid protein, 60 copies of the penton protein and 1800 minor capsid proteins of which there are 13 different types. The minor capsid proteins form a hexagonal network below the outer capsid shell, stabilizing the capsid by binding neighboring capsomers together. The size of the viral capsid is determined by a tape-measure, minor capsid protein of which there are 60 copies in the virion. Homologs of the tape-measure protein and some of the other minor capsid proteins exist in other NCLDVs. Thus, a similar capsid assembly pathway might be used by other NCLDVs.

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Disease

Primary Citation of related structures