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- EMDB-23388: Structure of human transfer RNA visualized in the cytomegalovirus... -

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Basic information

Entry
Database: EMDB / ID: EMD-23388
TitleStructure of human transfer RNA visualized in the cytomegalovirus, a DNA virus
Map dataC2 2-fold sub-particle reconstruction of HCMV virion particles
Sample
  • Complex: Transfer RNA visualized in the cytomegalovirus, a DNA virus
    • Complex: RNA
      • RNA: RNA (75-MER)
    • Virus: Human herpesvirus 5 strain AD169
      • Protein or peptide: Tegument protein pp150
KeywordsHCMV / tRNA / VIRUS
Function / homologyhost cell viral assembly compartment / Herpesvirus UL11/UL32 / Herpesvirus large structural phosphoprotein UL32 / viral tegument / host cell cytoplasmic vesicle / host cell perinuclear region of cytoplasm / host cell nucleus / structural molecule activity / Large structural phosphoprotein
Function and homology information
Biological speciesHomo sapiens (human) / Human cytomegalovirus (strain AD169) / Human herpesvirus 5 strain AD169
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLiu YT / Strugatsky D
Funding support United States, 5 items
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, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lj3
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7lj3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23388.png

Downloads & links

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Map

FileDownload / File: emd_23388.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC2 2-fold sub-particle reconstruction of HCMV virion particles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.07530269 - 0.12552957
Average (Standard dev.)0.0024589403 (±0.009601027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z435.200435.200435.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ376376376
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.0750.1260.002

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Supplemental data

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Sample components

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Entire : Transfer RNA visualized in the cytomegalovirus, a DNA virus

EntireName: Transfer RNA visualized in the cytomegalovirus, a DNA virus
Components
  • Complex: Transfer RNA visualized in the cytomegalovirus, a DNA virus
    • Complex: RNA
      • RNA: RNA (75-MER)
    • Virus: Human herpesvirus 5 strain AD169
      • Protein or peptide: Tegument protein pp150

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Supramolecule #1: Transfer RNA visualized in the cytomegalovirus, a DNA virus

SupramoleculeName: Transfer RNA visualized in the cytomegalovirus, a DNA virus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Human herpesvirus 5 strain AD169

SupramoleculeName: Human herpesvirus 5 strain AD169 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1 / NCBI-ID: 10360 / Sci species name: Human herpesvirus 5 strain AD169 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Tegument protein pp150

MacromoleculeName: Tegument protein pp150 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Human cytomegalovirus (strain AD169) / Strain: AD169
Molecular weightTheoretical: 33.232418 KDa
SequenceString: MSLQFIGLQR RDVVALVNFL RHLTQKPDVD LEAHPKILKK CGEKRLHRRT VLFNELMLWL GYYRELRFHN PDLSSVLEEF EVRCVAVAR RGYTYPFGDR GKARDHLAVL DRTEFDTDVR HDAEIVERAL VSAVILAKMS VRETLVTAIG QTEPIAFVHL K DTEVQRIE ...String:
MSLQFIGLQR RDVVALVNFL RHLTQKPDVD LEAHPKILKK CGEKRLHRRT VLFNELMLWL GYYRELRFHN PDLSSVLEEF EVRCVAVAR RGYTYPFGDR GKARDHLAVL DRTEFDTDVR HDAEIVERAL VSAVILAKMS VRETLVTAIG QTEPIAFVHL K DTEVQRIE ENLEGVRRNM FCVKPLDLNL DRHANTALVN AVNKLVYTGR LIMNVRRSWE ELERKCLARI QERCKLLVKE LR MCLSFDS NYCRNILKHA VENGDSADTL LELLIEDFDI YVDSFPQS

UniProtKB: Large structural phosphoprotein

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Macromolecule #2: RNA (75-MER)

MacromoleculeName: RNA (75-MER) / type: rna / ID: 2 / Number of copies: 3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.077223 KDa
SequenceString:
UCCCUGGUGG UCUAGUGGUU AGGAUUCGGC GCUCUCACCG CCGCGGCCCG GGUUCGAUUC CCGGUCAGGG AACCA

GENBANK: GENBANK: M31637.1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43666
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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