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- PDB-7lj3: Structure of human transfer RNA visualized in the cytomegalovirus... -

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Basic information

Entry
Database: PDB / ID: 7lj3
TitleStructure of human transfer RNA visualized in the cytomegalovirus, a DNA virus
Components
  • RNA (75-MER)
  • Tegument protein pp150
KeywordsVIRUS / HCMV / tRNA
Function / homology
Function and homology information


host cell viral assembly compartment / viral tegument / host cell cytoplasmic vesicle / host cell perinuclear region of cytoplasm / host cell nucleus / structural molecule activity
Similarity search - Function
Herpesvirus UL11/UL32 / Herpesvirus large structural phosphoprotein UL32
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Large structural phosphoprotein
Similarity search - Component
Biological speciesHuman cytomegalovirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLiu, Y.T. / Strugatsky, D. / Liu, W. / Zhou, Z.H.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583/DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1U24GM116792 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1S10OD018111 United States
National Science Foundation (NSF, United States)DBI-1338135 and DMR-1548924 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structure of human cytomegalovirus virion reveals host tRNA binding to capsid-associated tegument protein pp150.
Authors: Yun-Tao Liu / David Strugatsky / Wei Liu / Z Hong Zhou /
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. ...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.
History
DepositionJan 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
z: Tegument protein pp150
0: Tegument protein pp150
y: Tegument protein pp150
5: Tegument protein pp150
6: Tegument protein pp150
4: Tegument protein pp150
8: Tegument protein pp150
9: Tegument protein pp150
7: Tegument protein pp150
A: RNA (75-MER)
B: RNA (75-MER)
C: RNA (75-MER)


Theoretical massNumber of molelcules
Total (without water)371,32312
Polymers371,32312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11050 Å2
ΔGint-37 kcal/mol
Surface area169650 Å2

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Components

#1: Protein
Tegument protein pp150 / 150 kDa matrix phosphoprotein / 150 kDa phosphoprotein / pp150 / Basic phosphoprotein / BPP / ...150 kDa matrix phosphoprotein / 150 kDa phosphoprotein / pp150 / Basic phosphoprotein / BPP / Phosphoprotein UL32 / Tegument protein UL32


Mass: 33232.418 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus (strain AD169) / Strain: AD169 / References: UniProt: P08318
#2: RNA chain RNA (75-MER)


Mass: 24077.223 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: M31637

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Transfer RNA visualized in the cytomegalovirus, a DNA virusCOMPLEXall0MULTIPLE SOURCES
2Tegument protein pp150VIRUS#11NATURAL
3RNACOMPLEX#21NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Human herpesvirus 5 strain AD16910360
23Homo sapiens (human)9606
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43666 / Symmetry type: POINT

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