8H2I

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Near-atomic, non-icosahedrally averaged structure of giant virus Paramecium bursaria chlorella virus 1.

Shao, Q.Agarkova, I.V.Noel, E.A.Dunigan, D.D.Liu, Y.Wang, A.Guo, M.Xie, L.Zhao, X.Rossmann, M.G.Van Etten, J.L.Klose, T.Fang, Q.

(2022) Nat Commun 13: 6476-6476

  • DOI: https://doi.org/10.1038/s41467-022-34218-4
  • Primary Citation of Related Structures:  
    8H2I

  • PubMed Abstract: 

    Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play critical roles in the viral life cycles, identities and high-resolution structures of these components remain unknown. Here, by determining a near-atomic-resolution, five-fold averaged structure of Paramecium bursaria chlorella virus 1, we unexpectedly found the viral capsid possesses up to five major capsid protein variants and a penton protein variant. These variants create varied capsid microenvironments for the associations of fibers, a vesicle, and previously unresolved minor capsid proteins. Our structure reveals the identities and atomic models of the capsid components that do not obey the overall icosahedral symmetry and leads to a model for how these components are assembled and initiate capsid assembly, and this model might be applicable to many other giant viruses.


  • Organizational Affiliation

    Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein (MCP)437Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MCPv1520Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
Find proteins for O41104 (Paramecium bursaria Chlorella virus 1)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MCPv2CC [auth bC]486Paramecium bursaria Chlorella virus 1Mutation(s): 1 
UniProt
Find proteins for M1I493 (Paramecium bursaria Chlorella virus NE-JV-4)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MCPv3403Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
MCPv4EC [auth bE],
EF [auth de],
QF [auth dq],
YE [auth cY]
401Paramecium bursaria Chlorella virus 1Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
P1v1GC [auth bG]530Paramecium bursaria Chlorella virus 1Mutation(s): 3 
UniProt
Find proteins for M1I677 (Paramecium bursaria Chlorella virus IL3A)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
P2HC [auth bH]576Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
P3IC [auth bI],
JC [auth bJ],
KC [auth bK]
171Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
P4LC [auth bL],
MC [auth bM],
NC [auth bN],
OC [auth bO]
181Paramecium bursaria Chlorella virus 1Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
P5PC [auth bP]146Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
P6QC [auth bQ]216Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
P8RC [auth bR]173Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
P9SC [auth bS]210Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
P11207Paramecium bursaria Chlorella virus 1Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
P12FD [auth cf]151Paramecium bursaria Chlorella virus 1Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
P13GD [auth cg]98Paramecium bursaria Chlorella virus 1Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
P15HD [auth ch]155Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
P16ID [auth ci]93Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
Find proteins for Q98530 (Paramecium bursaria Chlorella virus 1)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
P17JD [auth cj],
KD [auth ck],
LD [auth cl],
MD [auth cm]
80Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
Find proteins for Q84629 (Paramecium bursaria Chlorella virus 1)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
P18ND [auth cn],
OD [auth co]
148Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
Find proteins for Q84533 (Paramecium bursaria Chlorella virus 1)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
P19378Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
Find proteins for Q84602 (Paramecium bursaria Chlorella virus 1)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
P201,335Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
Find proteins for Q89353 (Paramecium bursaria Chlorella virus 1)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
P21BF [auth db],
HF [auth dh],
PE [auth cP],
TF [auth dt]
1,369Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
MCPv5RE [auth cR],
SE [auth cS],
TE [auth cT]
400Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
P22UE [auth cU],
VE [auth cV],
WE [auth cW]
1,343Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
Find proteins for Q84443 (Paramecium bursaria Chlorella virus 1)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
P23MF [auth dm],
NF [auth dn],
OF [auth do]
1,359Paramecium bursaria Chlorella virus 1Mutation(s): 0 
UniProt
Find proteins for Q89360 (Paramecium bursaria Chlorella virus 1)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1736030
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: 2022-11-16
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references