6W2E

Structures of Capsid and Capsid-Associated Tegument Complex inside the Epstein-Barr Virus

  • Classification: VIRAL PROTEIN
  • Organism(s): Human herpesvirus 4 strain B95-8
  • Mutation(s): No 

  • Deposited: 2020-03-05 Released: 2020-07-15 
  • Deposition Author(s): Liu, W., Cui, Y.X., Wang, C.Y., Li, Z.H., Gong, D.Y., Dai, X.H., Bi, G.Q., Sun, R., Zhou, Z.H.
  • Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus.

Liu, W.Cui, Y.Wang, C.Li, Z.Gong, D.Dai, X.Bi, G.Q.Sun, R.Zhou, Z.H.

(2020) Nat Microbiol 5: 1285-1298

  • DOI: https://doi.org/10.1038/s41564-020-0758-1
  • Primary Citation of Related Structures:  
    6W19, 6W2D, 6W2E

  • PubMed Abstract: 

    As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been hindered by latency-a hallmark of EBV infection-and atomic structures are thus available only for recombinantly expressed EBV proteins. In the present study, by symmetry relaxation and subparticle reconstruction, we have determined near-atomic-resolution structures of the EBV capsid with an asymmetrically attached DNA-translocating portal and capsid-associated tegument complexes from cryogenic electron microscopy images of just 2,048 EBV virions obtained by chemical induction. The resulting atomic models reveal structural plasticity among the 20 conformers of the major capsid protein, 2 conformers of the small capsid protein (SCP), 4 conformers of the triplex monomer proteins and 2 conformers of the triplex dimer proteins. Plasticity reaches the greatest level at the capsid-tegument interfaces involving SCP and capsid-associated tegument complexes (CATC): SCPs crown pentons/hexons and mediate tegument protein binding, and CATCs bind and rotate all five periportal triplexes, but notably only about one peri-penton triplex. These results offer insights into the EBV capsid assembly and a mechanism for recruiting cell-regulating factors into the tegument compartment as 'cargoes', and should inform future anti-EBV strategies.


  • Organizational Affiliation

    California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid proteinA [auth J],
B [auth K],
C [auth N],
D [auth O]
1,381Human herpesvirus 4 strain B95-8Mutation(s): 0 
UniProt
Find proteins for P03226 (Epstein-Barr virus (strain B95-8))
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Go to UniProtKB:  P03226
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UniProt GroupP03226
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid vertex component 1E [auth v]507Human herpesvirus 4 strain B95-8Mutation(s): 0 
UniProt
Find proteins for P03222 (Epstein-Barr virus (strain B95-8))
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UniProt GroupP03222
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid vertex component 2F [auth w],
G [auth x]
570Human herpesvirus 4 strain B95-8Mutation(s): 0 
UniProt
Find proteins for P03233 (Epstein-Barr virus (strain B95-8))
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Go to UniProtKB:  P03233
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UniProt GroupP03233
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large tegument protein deneddylaseH [auth y],
I [auth z]
3,149Human herpesvirus 4 strain B95-8Mutation(s): 0 
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P03186 (Epstein-Barr virus (strain B95-8))
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UniProt GroupP03186
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small capsomere-interacting proteinJ [auth Z],
K [auth a],
L [auth d],
M [auth e]
176Human herpesvirus 4 strain B95-8Mutation(s): 0 
UniProt
Find proteins for P14348 (Epstein-Barr virus (strain B95-8))
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Go to UniProtKB:  P14348
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UniProt GroupP14348
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 1N [auth f],
O [auth h]
364Human herpesvirus 4 strain B95-8Mutation(s): 0 
UniProt
Find proteins for P03187 (Epstein-Barr virus (strain B95-8))
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UniProt GroupP03187
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 2P [auth k],
Q [auth m],
R [auth p],
S [auth r]
301Human herpesvirus 4 strain B95-8Mutation(s): 0 
UniProt
Find proteins for P25214 (Epstein-Barr virus (strain B95-8))
Explore P25214 
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UniProt GroupP25214
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesDE028583, DE025567
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI094386
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1S10RR23057, 1S10OD018111, and 1U24GM116792
National Science Foundation (NSF, United States)United StatesDBI-1338135 and DMR-1548924

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2020-10-07
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references