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 1.0 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 ...

    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

    Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA. fangqlin3@mail.sysu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid protein (MCP)437Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A430L
UniProt
Find proteins for P30328 (Paramecium bursaria Chlorella virus 1)
Explore P30328 
Go to UniProtKB:  P30328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30328
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MCPv1520Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A622L
UniProt
Find proteins for O41104 (Paramecium bursaria Chlorella virus 1)
Explore O41104 
Go to UniProtKB:  O41104
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO41104
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MCPv2CC [auth bC]486Paramecium bursaria Chlorella virus 1Mutation(s): 1 
UniProt
Find proteins for M1I493 (Paramecium bursaria Chlorella virus NE-JV-4)
Explore M1I493 
Go to UniProtKB:  M1I493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1I493
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MCPv3403Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A011L
UniProt
Find proteins for Q89346 (Paramecium bursaria Chlorella virus 1)
Explore Q89346 
Go to UniProtKB:  Q89346
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89346
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
MCPv4EC [auth bE],
EF [auth de],
QF [auth dq],
YE [auth cY]
401Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A010R
UniProt
Find proteins for Q89345 (Paramecium bursaria Chlorella virus 1)
Explore Q89345 
Go to UniProtKB:  Q89345
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89345
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
P1v1GC [auth bG]530Paramecium bursaria Chlorella virus 1Mutation(s): 3 
UniProt
Find proteins for M1I677 (Paramecium bursaria Chlorella virus IL3A)
Explore M1I677 
Go to UniProtKB:  M1I677
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1I677
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
P2HC [auth bH]576Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A342L
UniProt
Find proteins for Q84656 (Paramecium bursaria Chlorella virus 1)
Explore Q84656 
Go to UniProtKB:  Q84656
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84656
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
P3IC [auth bI],
JC [auth bJ],
KC [auth bK]
171Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A523R
UniProt
Find proteins for Q98573 (Paramecium bursaria Chlorella virus 1)
Explore Q98573 
Go to UniProtKB:  Q98573
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98573
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
P4LC [auth bL],
MC [auth bM],
NC [auth bN],
OC [auth bO]
181Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A572R
UniProt
Find proteins for O41054 (Paramecium bursaria Chlorella virus 1)
Explore O41054 
Go to UniProtKB:  O41054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO41054
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
P5PC [auth bP]146Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A526R
UniProt
Find proteins for Q98576 (Paramecium bursaria Chlorella virus 1)
Explore Q98576 
Go to UniProtKB:  Q98576
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98576
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
P6QC [auth bQ]216Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A203R
UniProt
Find proteins for Q84523 (Paramecium bursaria Chlorella virus 1)
Explore Q84523 
Go to UniProtKB:  Q84523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84523
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
P8RC [auth bR]173Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A644R
UniProt
Find proteins for O41126 (Paramecium bursaria Chlorella virus 1)
Explore O41126 
Go to UniProtKB:  O41126
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO41126
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
P9SC [auth bS]210Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A407L
UniProt
Find proteins for Q98459 (Paramecium bursaria Chlorella virus 1)
Explore Q98459 
Go to UniProtKB:  Q98459
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98459
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
P11207Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A352L
UniProt
Find proteins for Q84666 (Paramecium bursaria Chlorella virus 1)
Explore Q84666 
Go to UniProtKB:  Q84666
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84666
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
P12FD [auth cf]151Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A139L
UniProt
Find proteins for Q84459 (Paramecium bursaria Chlorella virus 1)
Explore Q84459 
Go to UniProtKB:  Q84459
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84459
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
P13GD [auth cg]98Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A421R
UniProt
Find proteins for Q98473 (Paramecium bursaria Chlorella virus 1)
Explore Q98473 
Go to UniProtKB:  Q98473
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98473
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
P15HD [auth ch]155Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A484L
UniProt
Find proteins for Q98534 (Paramecium bursaria Chlorella virus 1)
Explore Q98534 
Go to UniProtKB:  Q98534
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98534
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
P16ID [auth ci]93Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A480L
UniProt
Find proteins for Q98530 (Paramecium bursaria Chlorella virus 1)
Explore Q98530 
Go to UniProtKB:  Q98530
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98530
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
P17JD [auth cj],
KD [auth ck],
LD [auth cl],
MD [auth cm]
80Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A314R
UniProt
Find proteins for Q84629 (Paramecium bursaria Chlorella virus 1)
Explore Q84629 
Go to UniProtKB:  Q84629
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84629
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
P18ND [auth cn],
OD [auth co]
148Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A213L
UniProt
Find proteins for Q84533 (Paramecium bursaria Chlorella virus 1)
Explore Q84533 
Go to UniProtKB:  Q84533
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84533
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
P19378Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A286R
UniProt
Find proteins for Q84602 (Paramecium bursaria Chlorella virus 1)
Explore Q84602 
Go to UniProtKB:  Q84602
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84602
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
P201,335Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A018L
UniProt
Find proteins for Q89353 (Paramecium bursaria Chlorella virus 1)
Explore Q89353 
Go to UniProtKB:  Q89353
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89353
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
P21BF [auth db],
HF [auth dh],
PE [auth cP],
TF [auth dt]
1,369Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A014R
UniProt
Find proteins for Q89349 (Paramecium bursaria Chlorella virus 1)
Explore Q89349 
Go to UniProtKB:  Q89349
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89349
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
MCPv5RE [auth cR],
SE [auth cS],
TE [auth cT]
400Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A558L
UniProt
Find proteins for O41040 (Paramecium bursaria Chlorella virus 1)
Explore O41040 
Go to UniProtKB:  O41040
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO41040
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
P22UE [auth cU],
VE [auth cV],
WE [auth cW]
1,343Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A122/123R
UniProt
Find proteins for Q84443 (Paramecium bursaria Chlorella virus 1)
Explore Q84443 
Go to UniProtKB:  Q84443
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84443
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
P23MF [auth dm],
NF [auth dn],
OF [auth do]
1,359Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A025/027/029L
UniProt
Find proteins for Q89360 (Paramecium bursaria Chlorella virus 1)
Explore Q89360 
Go to UniProtKB:  Q89360
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89360
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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