7BR7

Epstein-Barr virus, C1 portal-proximal penton vertex, CATC binding

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

  • Deposited: 2020-03-26 Released: 2020-09-30 
  • Deposition Author(s): Li, Z., Yu, X.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 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

CryoEM structure of the tegumented capsid of Epstein-Barr virus.

Li, Z.Zhang, X.Dong, L.Pang, J.Xu, M.Zhong, Q.Zeng, M.S.Yu, X.

(2020) Cell Res 30: 873-884

  • DOI: https://doi.org/10.1038/s41422-020-0363-0
  • Primary Citation of Related Structures:  
    7BQT, 7BQX, 7BR7, 7BR8, 7BSI

  • PubMed Abstract: 

    Epstein-Barr virus (EBV) is the primary cause of infectious mononucleosis and has been shown to be closely associated with various malignancies. Here, we present a complete atomic model of EBV, including the icosahedral capsid, the dodecameric portal and the capsid-associated tegument complex (CATC). Our in situ portal from the tegumented capsid adopts a closed conformation with its channel valve holding the terminal viral DNA and with its crown region firmly engaged by three layers of ring-like dsDNA, which, together with the penton flexibility, effectively alleviates the capsid inner pressure placed on the portal cap. In contrast, the CATCs, through binding to the flexible penton vertices in a stoichiometric manner, accurately increase the inner capsid pressure to facilitate the pressure-driven genome delivery. Together, our results provide important insights into the mechanism by which the EBV capsid, portal, packaged genome and the CATCs coordinately achieve a pressure balance to simultaneously benefit both viral genome retention and ejection.


  • Organizational Affiliation

    Cryo-Electron Microscopy Research Center, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid vertex component 2A [auth K],
B [auth G]
570Human herpesvirus 4 strain B95-8Mutation(s): 0 
UniProt
Find proteins for P03233 (Epstein-Barr virus (strain B95-8))
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UniProt GroupP03233
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid vertex component 1507Human 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
Large tegument protein deneddylaseD [auth B],
E [auth O]
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small capsomere-interacting proteinF [auth m],
G [auth Y],
H [auth Z],
I [auth 2],
N [auth y]
176Human herpesvirus 4 strain B95-8Mutation(s): 0 
UniProt
Find proteins for P14348 (Epstein-Barr virus (strain B95-8))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid proteinJ [auth S],
K [auth T],
L [auth W],
M [auth x],
R [auth l]
1,381Human herpesvirus 4 strain B95-8Mutation(s): 0 
UniProt
Find proteins for P03226 (Epstein-Barr virus (strain B95-8))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 1O [auth e],
S [auth 5]
364Human herpesvirus 4 strain B95-8Mutation(s): 0 
UniProt
Find proteins for P03187 (Epstein-Barr virus (strain B95-8))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 2P [auth f],
Q [auth g],
T [auth 6],
U [auth 7]
301Human herpesvirus 4 strain B95-8Mutation(s): 0 
UniProt
Find proteins for P25214 (Epstein-Barr virus (strain B95-8))
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UniProt GroupP25214
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2020-09-30 
  • Deposition Author(s): Li, Z., Yu, X.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31900869
National Natural Science Foundation of China (NSFC)China81830090
National Natural Science Foundation of China (NSFC)China81702001
Ministry of Science and Technology (MoST, China)China2017YFA0505600
Ministry of Science and Technology (MoST, China)China2016YFA0502101

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references