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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 / homologyMajor capsid protein, C-terminal / Hexon coat protein, subdomain 4 / Group II dsDNA virus coat/capsid protein / Major capsid protein, N-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Major capsid protein N-terminus / viral capsid / structural molecule activity / integral component of membrane ...Major capsid protein, C-terminal / Hexon coat protein, subdomain 4 / Group II dsDNA virus coat/capsid protein / Major capsid protein, N-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Major capsid protein N-terminus / viral capsid / structural molecule activity / integral component of membrane / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Major capsid protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Specimen sourceParamecium bursaria Chlorella virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsFang, Q. / Rossmann, M.G.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 11, 2018 / Release: Jan 30, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 30, 2019Structure modelrepositoryInitial release
1.1Feb 6, 2019Structure modelData collection / Database referencescitation_citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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
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  • Simplified surface model + fitted atomic model
  • EMDB-0436
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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
Polyers4,793,079115
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
Polyers287,584,7156900
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
Polyers23,965,393575
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
Polyers28,758,471690
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

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Components

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Protein/peptide , 15 types, 115 molecules a0a1a2a3a4a5a6a7a8a9b0b1b2b3b4b5b7b8c0c1l5b6c2c3c4c5c6c7c8c9...

#1: Protein/peptide P14


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 11070.830 Da / Num. of mol.: 1 / 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 / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Paramecium bursaria Chlorella virus 1 / Type: VIRUS / Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15 / Source: NATURAL
Source (natural)Organism: Paramecium bursaria Chlorella virus 1
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: OTHER / Virus 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
MicroscopyMicroscope model: 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
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 13000 / Symmetry type: POINT

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