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- PDB-6ncl: Near-atomic structure of icosahedrally averaged PBCV-1 capsid -

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Basic information

Entry
Database: PDB / ID: 6ncl
TitleNear-atomic structure of icosahedrally averaged PBCV-1 capsid
Components
  • Major capsid protein
  • P1
  • P10
  • P11
  • P12
  • P13
  • P14
  • P2
  • P3
  • P4
  • P5
  • P6
  • P7
  • P8
  • P9
KeywordsVIRUS / tape-measure protein / minor capsid proteins / zip protein / giant virus
Function / homology
Function and homology information


viral capsid / membrane => GO:0016020 / structural molecule activity / membrane
Similarity search - Function
Protein of unknown function DUF5762 / Protein of unknown function DUF5761 / Domain of unknown function DUF5899 / Family of unknown function (DUF5761) / Family of unknown function (DUF5762) / Family of unknown function (DUF5899) / Major capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily ...Protein of unknown function DUF5762 / Protein of unknown function DUF5761 / Domain of unknown function DUF5899 / Family of unknown function (DUF5761) / Family of unknown function (DUF5762) / Family of unknown function (DUF5899) / Major capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Uncharacterized protein / Capsid protein / Major capsid protein / Uncharacterized protein / PsbP C-terminal domain-containing protein / Uncharacterized protein / Uncharacterized protein / DUF5899 domain-containing protein / Uncharacterized protein / SAYSvFN domain-containing protein ...Uncharacterized protein / Capsid protein / Major capsid protein / Uncharacterized protein / PsbP C-terminal domain-containing protein / Uncharacterized protein / Uncharacterized protein / DUF5899 domain-containing protein / Uncharacterized protein / SAYSvFN domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Capsid protein / Uncharacterized protein
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFang, Q. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Nat Commun / Year: 2019
Title: Near-atomic structure of a giant virus.
Authors: Qianglin Fang / Dongjie Zhu / Irina Agarkova / Jagat Adhikari / Thomas Klose / Yue Liu / Zhenguo Chen / Yingyuan Sun / Michael L Gross / James L Van Etten / Xinzheng Zhang / Michael G Rossmann /
Abstract: 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 ...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.
History
DepositionDec 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-0436
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-0436
  • Imaged by UCSF Chimera
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  • Superimposition on EM map
  • EMDB-0436
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
a0: P14
a1: P9
a2: P10
a3: P10
a4: P7
a5: P6
a6: P1
a7: P12
a8: P5
a9: P11
b0: P11
b1: P11
b2: P11
b3: P11
b4: P11
b5: P11
b6: P2
b7: P11
b8: P11
c0: P11
c1: P11
c2: P4
c3: P4
c4: P4
c5: P4
c6: P3
c7: P3
c8: P3
c9: P8
d0: Major capsid protein
d1: Major capsid protein
d2: Major capsid protein
d3: Major capsid protein
d4: Major capsid protein
d5: Major capsid protein
d6: Major capsid protein
d7: Major capsid protein
d8: Major capsid protein
d9: Major capsid protein
e0: Major capsid protein
e1: Major capsid protein
e2: Major capsid protein
e3: Major capsid protein
e4: Major capsid protein
e5: Major capsid protein
e6: Major capsid protein
e7: Major capsid protein
e8: Major capsid protein
e9: Major capsid protein
f0: Major capsid protein
f1: Major capsid protein
f2: Major capsid protein
f3: Major capsid protein
f4: Major capsid protein
f5: Major capsid protein
f6: Major capsid protein
f7: Major capsid protein
f8: Major capsid protein
f9: Major capsid protein
g0: Major capsid protein
g1: Major capsid protein
g2: Major capsid protein
g3: Major capsid protein
g4: Major capsid protein
g5: Major capsid protein
g6: Major capsid protein
g7: Major capsid protein
g8: Major capsid protein
g9: Major capsid protein
h0: Major capsid protein
h1: Major capsid protein
h2: Major capsid protein
h3: Major capsid protein
h4: Major capsid protein
h5: Major capsid protein
h6: Major capsid protein
h7: Major capsid protein
h8: Major capsid protein
h9: Major capsid protein
i0: Major capsid protein
i1: Major capsid protein
i2: Major capsid protein
i3: Major capsid protein
i4: Major capsid protein
i5: Major capsid protein
i6: Major capsid protein
i7: Major capsid protein
i8: Major capsid protein
i9: Major capsid protein
j0: Major capsid protein
j1: Major capsid protein
j2: Major capsid protein
j3: Major capsid protein
j4: Major capsid protein
j5: Major capsid protein
j6: Major capsid protein
j7: Major capsid protein
j8: Major capsid protein
j9: Major capsid protein
k0: Major capsid protein
k1: Major capsid protein
k2: Major capsid protein
k3: Major capsid protein
k4: Major capsid protein
k5: Major capsid protein
k6: Major capsid protein
k7: Major capsid protein
k8: Major capsid protein
k9: Major capsid protein
l0: Major capsid protein
l1: Major capsid protein
l2: Major capsid protein
l3: Major capsid protein
l4: P13
l5: P11


Theoretical massNumber of molelcules
Total (without water)4,793,079115
Polymers4,793,079115
Non-polymers00
Water0
1
a0: P14
a1: P9
a2: P10
a3: P10
a4: P7
a5: P6
a6: P1
a7: P12
a8: P5
a9: P11
b0: P11
b1: P11
b2: P11
b3: P11
b4: P11
b5: P11
b6: P2
b7: P11
b8: P11
c0: P11
c1: P11
c2: P4
c3: P4
c4: P4
c5: P4
c6: P3
c7: P3
c8: P3
c9: P8
d0: Major capsid protein
d1: Major capsid protein
d2: Major capsid protein
d3: Major capsid protein
d4: Major capsid protein
d5: Major capsid protein
d6: Major capsid protein
d7: Major capsid protein
d8: Major capsid protein
d9: Major capsid protein
e0: Major capsid protein
e1: Major capsid protein
e2: Major capsid protein
e3: Major capsid protein
e4: Major capsid protein
e5: Major capsid protein
e6: Major capsid protein
e7: Major capsid protein
e8: Major capsid protein
e9: Major capsid protein
f0: Major capsid protein
f1: Major capsid protein
f2: Major capsid protein
f3: Major capsid protein
f4: Major capsid protein
f5: Major capsid protein
f6: Major capsid protein
f7: Major capsid protein
f8: Major capsid protein
f9: Major capsid protein
g0: Major capsid protein
g1: Major capsid protein
g2: Major capsid protein
g3: Major capsid protein
g4: Major capsid protein
g5: Major capsid protein
g6: Major capsid protein
g7: Major capsid protein
g8: Major capsid protein
g9: Major capsid protein
h0: Major capsid protein
h1: Major capsid protein
h2: Major capsid protein
h3: Major capsid protein
h4: Major capsid protein
h5: Major capsid protein
h6: Major capsid protein
h7: Major capsid protein
h8: Major capsid protein
h9: Major capsid protein
i0: Major capsid protein
i1: Major capsid protein
i2: Major capsid protein
i3: Major capsid protein
i4: Major capsid protein
i5: Major capsid protein
i6: Major capsid protein
i7: Major capsid protein
i8: Major capsid protein
i9: Major capsid protein
j0: Major capsid protein
j1: Major capsid protein
j2: Major capsid protein
j3: Major capsid protein
j4: Major capsid protein
j5: Major capsid protein
j6: Major capsid protein
j7: Major capsid protein
j8: Major capsid protein
j9: Major capsid protein
k0: Major capsid protein
k1: Major capsid protein
k2: Major capsid protein
k3: Major capsid protein
k4: Major capsid protein
k5: Major capsid protein
k6: Major capsid protein
k7: Major capsid protein
k8: Major capsid protein
k9: Major capsid protein
l0: Major capsid protein
l1: Major capsid protein
l2: Major capsid protein
l3: Major capsid protein
l4: P13
l5: P11
x 60


  • complete icosahedral assembly
  • Evidence: microscopy
  • 288 MDa, 6900 polymers
Theoretical massNumber of molelcules
Total (without water)287,584,7156900
Polymers287,584,7156900
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
a0: P14
a1: P9
a2: P10
a3: P10
a4: P7
a5: P6
a6: P1
a7: P12
a8: P5
a9: P11
b0: P11
b1: P11
b2: P11
b3: P11
b4: P11
b5: P11
b6: P2
b7: P11
b8: P11
c0: P11
c1: P11
c2: P4
c3: P4
c4: P4
c5: P4
c6: P3
c7: P3
c8: P3
c9: P8
d0: Major capsid protein
d1: Major capsid protein
d2: Major capsid protein
d3: Major capsid protein
d4: Major capsid protein
d5: Major capsid protein
d6: Major capsid protein
d7: Major capsid protein
d8: Major capsid protein
d9: Major capsid protein
e0: Major capsid protein
e1: Major capsid protein
e2: Major capsid protein
e3: Major capsid protein
e4: Major capsid protein
e5: Major capsid protein
e6: Major capsid protein
e7: Major capsid protein
e8: Major capsid protein
e9: Major capsid protein
f0: Major capsid protein
f1: Major capsid protein
f2: Major capsid protein
f3: Major capsid protein
f4: Major capsid protein
f5: Major capsid protein
f6: Major capsid protein
f7: Major capsid protein
f8: Major capsid protein
f9: Major capsid protein
g0: Major capsid protein
g1: Major capsid protein
g2: Major capsid protein
g3: Major capsid protein
g4: Major capsid protein
g5: Major capsid protein
g6: Major capsid protein
g7: Major capsid protein
g8: Major capsid protein
g9: Major capsid protein
h0: Major capsid protein
h1: Major capsid protein
h2: Major capsid protein
h3: Major capsid protein
h4: Major capsid protein
h5: Major capsid protein
h6: Major capsid protein
h7: Major capsid protein
h8: Major capsid protein
h9: Major capsid protein
i0: Major capsid protein
i1: Major capsid protein
i2: Major capsid protein
i3: Major capsid protein
i4: Major capsid protein
i5: Major capsid protein
i6: Major capsid protein
i7: Major capsid protein
i8: Major capsid protein
i9: Major capsid protein
j0: Major capsid protein
j1: Major capsid protein
j2: Major capsid protein
j3: Major capsid protein
j4: Major capsid protein
j5: Major capsid protein
j6: Major capsid protein
j7: Major capsid protein
j8: Major capsid protein
j9: Major capsid protein
k0: Major capsid protein
k1: Major capsid protein
k2: Major capsid protein
k3: Major capsid protein
k4: Major capsid protein
k5: Major capsid protein
k6: Major capsid protein
k7: Major capsid protein
k8: Major capsid protein
k9: Major capsid protein
l0: Major capsid protein
l1: Major capsid protein
l2: Major capsid protein
l3: Major capsid protein
l4: P13
l5: P11
x 5


  • icosahedral pentamer
  • 24 MDa, 575 polymers
Theoretical massNumber of molelcules
Total (without water)23,965,393575
Polymers23,965,393575
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
a0: P14
a1: P9
a2: P10
a3: P10
a4: P7
a5: P6
a6: P1
a7: P12
a8: P5
a9: P11
b0: P11
b1: P11
b2: P11
b3: P11
b4: P11
b5: P11
b6: P2
b7: P11
b8: P11
c0: P11
c1: P11
c2: P4
c3: P4
c4: P4
c5: P4
c6: P3
c7: P3
c8: P3
c9: P8
d0: Major capsid protein
d1: Major capsid protein
d2: Major capsid protein
d3: Major capsid protein
d4: Major capsid protein
d5: Major capsid protein
d6: Major capsid protein
d7: Major capsid protein
d8: Major capsid protein
d9: Major capsid protein
e0: Major capsid protein
e1: Major capsid protein
e2: Major capsid protein
e3: Major capsid protein
e4: Major capsid protein
e5: Major capsid protein
e6: Major capsid protein
e7: Major capsid protein
e8: Major capsid protein
e9: Major capsid protein
f0: Major capsid protein
f1: Major capsid protein
f2: Major capsid protein
f3: Major capsid protein
f4: Major capsid protein
f5: Major capsid protein
f6: Major capsid protein
f7: Major capsid protein
f8: Major capsid protein
f9: Major capsid protein
g0: Major capsid protein
g1: Major capsid protein
g2: Major capsid protein
g3: Major capsid protein
g4: Major capsid protein
g5: Major capsid protein
g6: Major capsid protein
g7: Major capsid protein
g8: Major capsid protein
g9: Major capsid protein
h0: Major capsid protein
h1: Major capsid protein
h2: Major capsid protein
h3: Major capsid protein
h4: Major capsid protein
h5: Major capsid protein
h6: Major capsid protein
h7: Major capsid protein
h8: Major capsid protein
h9: Major capsid protein
i0: Major capsid protein
i1: Major capsid protein
i2: Major capsid protein
i3: Major capsid protein
i4: Major capsid protein
i5: Major capsid protein
i6: Major capsid protein
i7: Major capsid protein
i8: Major capsid protein
i9: Major capsid protein
j0: Major capsid protein
j1: Major capsid protein
j2: Major capsid protein
j3: Major capsid protein
j4: Major capsid protein
j5: Major capsid protein
j6: Major capsid protein
j7: Major capsid protein
j8: Major capsid protein
j9: Major capsid protein
k0: Major capsid protein
k1: Major capsid protein
k2: Major capsid protein
k3: Major capsid protein
k4: Major capsid protein
k5: Major capsid protein
k6: Major capsid protein
k7: Major capsid protein
k8: Major capsid protein
k9: Major capsid protein
l0: Major capsid protein
l1: Major capsid protein
l2: Major capsid protein
l3: Major capsid protein
l4: P13
l5: P11
x 6


  • icosahedral 23 hexamer
  • 28.8 MDa, 690 polymers
Theoretical massNumber of molelcules
Total (without water)28,758,471690
Polymers28,758,471690
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 15 types, 115 molecules a0a1a2a3a4a5a6a7a8a9b0b1b2b3b4b5b7b8c0c1l5b6c2c3c4c5c6c7c8c9...

#1: Protein P14


Mass: 38502.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98550
#2: Protein P9


Mass: 23407.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98459
#3: Protein P10


Mass: 31223.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98505
#4: Protein P7


Mass: 29505.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84580
#5: Protein P6


Mass: 24036.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84523
#6: Protein P1


Mass: 18281.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84626
#7: Protein P12


Mass: 17715.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84459
#8: Protein P5


Mass: 16455.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98576
#9: Protein
P11


Mass: 23322.656 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84666
#10: Protein P2


Mass: 63888.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84656
#11: Protein
P4


Mass: 20637.311 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: O41054
#12: Protein P3


Mass: 19116.688 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98573
#13: Protein P8


Mass: 19226.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: O41126
#14: Protein ...
Major capsid protein / MCP / VP54


Mass: 48199.625 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: P30328
#15: Protein P13


Mass: 11070.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98473

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Paramecium bursaria Chlorella virus 1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Paramecium bursaria Chlorella virus 1
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 85 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 24.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13000 / Symmetry type: POINT

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