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

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Basic information

Entry
Database: PDB / ID: 7liv
TitleStructure of human transfer RNA visualized in the cytomegalovirus, a DNA virus
Components
  • Major capsid protein
  • Small capsomere-interacting protein
  • Tegument protein pp150
  • Triplex capsid protein 1
  • Triplex capsid protein 2
KeywordsVIRUS / HCMV / tRNA
Function / homology
Function and homology information


host cell viral assembly compartment / T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / host cell cytoplasmic vesicle / viral process / viral capsid / host cell perinuclear region of cytoplasm / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Herpesvirus UL11/UL32 / Herpesvirus large structural phosphoprotein UL32 / Small capsid protein, Herpesviridae / Small capsid protein of Herpesviridae / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid protein 2 / Herpesvirus VP23 like capsid protein / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein
Similarity search - Domain/homology
Large structural phosphoprotein / Triplex capsid protein 2 / Major capsid protein / Triplex capsid protein 1 / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman cytomegalovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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) 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 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Assembly

Deposited unit
J: Major capsid protein
A: Major capsid protein
C: Major capsid protein
5: Tegument protein pp150
6: Tegument protein pp150
4: Tegument protein pp150
Z: Small capsomere-interacting protein
D: Small capsomere-interacting protein
E: Small capsomere-interacting protein
p: Triplex capsid protein 1
q: Triplex capsid protein 2
r: Triplex capsid protein 2


Theoretical massNumber of molelcules
Total (without water)689,67512
Polymers689,67512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area53130 Å2
ΔGint-324 kcal/mol
Surface area246700 Å2

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Components

#1: Protein Major capsid protein / MCP


Mass: 154048.906 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus (strain AD169) / Strain: AD169 / References: UniProt: P16729
#2: 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.: 3 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus (strain AD169) / Strain: AD169 / References: UniProt: P08318
#3: Protein Small capsomere-interacting protein / Smallest capsid protein / SCP


Mass: 8495.924 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus (strain AD169) / Strain: AD169 / References: UniProt: Q7M6N6
#4: Protein Triplex capsid protein 1 / Triplex monomer protein / Tri1


Mass: 33071.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus (strain AD169) / Strain: AD169 / References: UniProt: P16783
#5: Protein Triplex capsid protein 2 / Triplex dimer protein / Tri2


Mass: 34635.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus (strain AD169) / Strain: AD169 / References: UniProt: P16728
Has protein modificationY

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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

ComponentName: Human cytomegalovirus (strain AD169) / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Human cytomegalovirus (strain AD169) / Strain: AD169
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: 18.9 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97166 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00948092
ELECTRON MICROSCOPYf_angle_d0.91365374
ELECTRON MICROSCOPYf_dihedral_angle_d15.81129154
ELECTRON MICROSCOPYf_chiral_restr0.057563
ELECTRON MICROSCOPYf_plane_restr0.0068405

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