8TES

Human cytomegalovirus portal vertex, virion configuration 2 (VC2)

  • Classification: VIRUS
  • Organism(s): Human herpesvirus 5 strain AD169
  • Mutation(s): No 

  • Deposited: 2023-07-06 Released: 2024-03-06 
  • Deposition Author(s): Jih, J., Liu, Y.T., Liu, W., Zhou, H.
  • Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR), National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), James B. Pendleton Charitable Trust (to the UCLA AIDS Institute), McCarthy Family Foundation (to the UCLA AIDS Institute), National Institutes of Health/Office of the Director, National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 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

The incredible bulk: Human cytomegalovirus tegument architectures uncovered by AI-empowered cryo-EM.

Jih, J.Liu, Y.T.Liu, W.Zhou, Z.H.

(2024) Sci Adv 10: eadj1640-eadj1640

  • DOI: https://doi.org/10.1126/sciadv.adj1640
  • Primary Citation of Related Structures:  
    8TEP, 8TES, 8TET, 8TEU, 8TEW

  • PubMed Abstract: 

    The compartmentalization of eukaryotic cells presents considerable challenges to the herpesvirus life cycle. The herpesvirus tegument, a bulky proteinaceous aggregate sandwiched between herpesviruses' capsid and envelope, is uniquely evolved to address these challenges, yet tegument structure and organization remain poorly characterized. We use deep-learning-enhanced cryogenic electron microscopy to investigate the tegument of human cytomegalovirus virions and noninfectious enveloped particles (NIEPs; a genome packaging-aborted state), revealing a portal-biased tegumentation scheme. We resolve atomic structures of portal vertex-associated tegument (PVAT) and identify multiple configurations of PVAT arising from layered reorganization of pUL77, pUL48 (large tegument protein), and pUL47 (inner tegument protein) assemblies. Analyses show that pUL77 seals the last-packaged viral genome end through electrostatic interactions, pUL77 and pUL48 harbor a head-linker-capsid-binding motif conducive to PVAT reconfiguration, and pUL47/48 dimers form 45-nm-long filaments extending from the portal vertex. These results provide a structural framework for understanding how herpesvirus tegument facilitates and evolves during processes spanning viral genome packaging to delivery.


  • Organizational Affiliation

    Molecular Biology Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large tegument protein deneddylaseA,
B [auth C]
2,241Human herpesvirus 5 strain AD169Mutation(s): 0 
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P16785 (Human cytomegalovirus (strain AD169))
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UniProt GroupP16785
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid vertex component 2C [auth E],
D [auth F]
642Human herpesvirus 5 strain AD169Mutation(s): 0 
UniProt
Find proteins for P16726 (Human cytomegalovirus (strain AD169))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid vertex component 1E [auth G]594Human herpesvirus 5 strain AD169Mutation(s): 0 
UniProt
Find proteins for P16799 (Human cytomegalovirus (strain AD169))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein1,370Human herpesvirus 5 strain AD169Mutation(s): 0 
UniProt
Find proteins for P16729 (Human cytomegalovirus (strain AD169))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small capsomere-interacting protein75Human herpesvirus 5 strain AD169Mutation(s): 0 
UniProt
Find proteins for Q7M6N6 (Human cytomegalovirus (strain AD169))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 1R [auth T],
U [auth W]
290Human herpesvirus 5 strain AD169Mutation(s): 0 
UniProt
Find proteins for P16783 (Human cytomegalovirus (strain AD169))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 2S [auth U],
T [auth V],
V [auth X],
W [auth Y]
306Human herpesvirus 5 strain AD169Mutation(s): 0 
UniProt
Find proteins for P16728 (Human cytomegalovirus (strain AD169))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large structural phosphoproteinX [auth Z]1,048Human herpesvirus 5 strain AD169Mutation(s): 0 
UniProt
Find proteins for P08318 (Human cytomegalovirus (strain AD169))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTISOLDE
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesDE028583
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesT32AR071307
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP30 AI152501
James B. Pendleton Charitable Trust (to the UCLA AIDS Institute)United States--
McCarthy Family Foundation (to the UCLA AIDS Institute)United States--
National Institutes of Health/Office of the DirectorUnited States1S10RR23057
National Institutes of Health/Office of the DirectorUnited States1S10OD018111
National Science Foundation (NSF, United States)United StatesDBI-1338135
National Science Foundation (NSF, United States)United StatesDMR-1548924

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release