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- EMDB-23377: Structure of human transfer RNA visualized in the cytomegalovirus... -

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Basic information

Entry
Database: EMDB / ID: EMD-23377
TitleStructure of human transfer RNA visualized in the cytomegalovirus, a DNA virus
Map dataC3 3-fold sub-particle reconstruction of HCMV virion particles
SampleTransfer RNA visualized in the cytomegalovirus != Human herpesvirus 5 strain AD169

Transfer RNA visualized in the cytomegalovirus

  • Virus: Human herpesvirus 5 strain AD169
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 herpesvirus 5 strain AD169
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu YT / Strugatsky D / Liu W / Zhou ZH
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, 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 27, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing 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
  • Download
  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23377.png

Downloads & links

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Map

FileDownload / File: emd_23377.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC3 3-fold sub-particle reconstruction of HCMV virion particles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.61 Å/pix.
x 256 pix.
= 412.16 Å		1.61 Å/pix.
x 256 pix.
= 412.16 Å		1.61 Å/pix.
x 256 pix.
= 412.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.61 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.057479523 - 0.10674679
Average (Standard dev.)0.0029939928 (±0.007444295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 412.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.611.611.61
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z412.160412.160412.160
α/β/γ90.00090.00090.000
start NX/NY/NZ989663
NX/NY/NZ108125172
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.0570.1070.003

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Supplemental data

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Sample components

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Entire : Transfer RNA visualized in the cytomegalovirus

EntireName: Transfer RNA visualized in the cytomegalovirus
Components
  • Virus: Human herpesvirus 5 strain AD169

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Supramolecule #1: Human herpesvirus 5 strain AD169

SupramoleculeName: Human herpesvirus 5 strain AD169 / type: virus / ID: 1 / Parent: 0 / 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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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: 18.9 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97166
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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