6NCL

Near-atomic structure of icosahedrally averaged PBCV-1 capsid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Near-atomic structure of a giant virus.

Fang, Q.Zhu, D.Agarkova, I.Adhikari, J.Klose, T.Liu, Y.Chen, Z.Sun, Y.Gross, M.L.Van Etten, J.L.Zhang, X.Rossmann, M.G.

(2019) Nat Commun 10: 388-388

  • DOI: 10.1038/s41467-019-08319-6
  • Primary Citation of Related Structures:  
    6NCL

  • PubMed 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 remained unknown. Here we describe a 3.5 Å resolution icosahedrally averaged capsid structure of Paramecium bursaria chlorella virus 1 (PBCV-1) ...

    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.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA. mr@purdue.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
P14A [auth a0]352Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A500L
UniProt
Find proteins for Q98550 (Paramecium bursaria Chlorella virus 1)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
P9B [auth a1]210Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A407L
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
P10C [auth a2],
D [auth a3]
289Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A454L
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
P7E [auth a4]256Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: 263LA262
UniProt
Find proteins for Q84580 (Paramecium bursaria Chlorella virus 1)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
P6F [auth a5]216Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A203R
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
P1G [auth a6]170Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A310L
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
P12H [auth a7]151Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A139L
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
P5I [auth a8]146Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A526R
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
P11207Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A352L
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
P2Q [auth b6]576Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A342L
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
P4V [auth c2],
W [auth c3],
X [auth c4],
Y [auth c5]
181Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A572R
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
P3Z [auth c6],
AA [auth c7],
BA [auth c8]
171Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A523R
UniProt
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Entity ID: 13
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P8CA [auth c9]173Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A644R
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid protein437Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A430L
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
P13JD [auth l4]98Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A421R
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI011219

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence