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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: Liu YT / Strugatsky D / Liu W / Zhou ZH
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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