7LIV

Structure of human transfer RNA visualized in the cytomegalovirus, a DNA virus

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

  • Deposited: 2021-01-28 Released: 2021-09-15 
  • Deposition Author(s): Liu, Y.T., Strugatsky, D., Liu, W., 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: 3.60 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

Structure of human cytomegalovirus virion reveals host tRNA binding to capsid-associated tegument protein pp150.

Liu, Y.T.Strugatsky, D.Liu, W.Zhou, Z.H.

(2021) Nat Commun 12: 5513-5513

  • DOI: https://doi.org/10.1038/s41467-021-25791-1
  • Primary Citation of Related Structures:  
    7LIV, 7LJ3

  • PubMed Abstract: 

    Under the Baltimore nucleic acid-based virus classification scheme, the herpesvirus human cytomegalovirus (HCMV) is a Class I virus, meaning that it contains a double-stranded DNA genome-and no RNA. Here, we report sub-particle cryoEM reconstructions of HCMV virions at 2.9 Å resolution revealing structures resembling non-coding transfer RNAs (tRNAs) associated with the virion's capsid-bound tegument protein, pp150. Through deep sequencing, we show that these RNA sequences match human tRNAs, and we built atomic models using the most abundant tRNA species. Based on our models, tRNA recruitment is mediated by the electrostatic interactions between tRNA phosphate groups and the helix-loop-helix motif of HCMV pp150. The specificity of these interactions may explain the absence of such tRNA densities in murine cytomegalovirus and other human herpesviruses.


  • Organizational Affiliation

    California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid proteinA [auth J],
B [auth A],
C
1,370Human herpesvirus 5 strain AD169Mutation(s): 0 
UniProt
Find proteins for P16729 (Human cytomegalovirus (strain AD169))
Explore P16729 
Go to UniProtKB:  P16729
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UniProt GroupP16729
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tegument protein pp150D [auth 5],
E [auth 6],
F [auth 4]
285Human herpesvirus 5 strain AD169Mutation(s): 0 
UniProt
Find proteins for P08318 (Human cytomegalovirus (strain AD169))
Explore P08318 
Go to UniProtKB:  P08318
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UniProt GroupP08318
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small capsomere-interacting proteinG [auth Z],
H [auth D],
I [auth E]
75Human herpesvirus 5 strain AD169Mutation(s): 0 
UniProt
Find proteins for Q7M6N6 (Human cytomegalovirus (strain AD169))
Explore Q7M6N6 
Go to UniProtKB:  Q7M6N6
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UniProt GroupQ7M6N6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 1J [auth p]290Human herpesvirus 5 strain AD169Mutation(s): 0 
UniProt
Find proteins for P16783 (Human cytomegalovirus (strain AD169))
Explore P16783 
Go to UniProtKB:  P16783
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UniProt GroupP16783
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 2K [auth q],
L [auth r]
306Human herpesvirus 5 strain AD169Mutation(s): 0 
UniProt
Find proteins for P16728 (Human cytomegalovirus (strain AD169))
Explore P16728 
Go to UniProtKB:  P16728
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UniProt GroupP16728
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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 States1U24GM116792
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1S10OD018111
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references