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- EMDB-24952: tRNA-like Structure from Brome Mosaic Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-24952
TitletRNA-like Structure from Brome Mosaic Virus
Map data
SampletRNA-like structure at the 3' UTR of the brome mosaic virus (BMV) genome:
nucleic-acidNucleic acid
Biological speciesBrome mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKieft JS / Bonilla SL
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118070 United States
National Science Foundation (NSF, United States)F32GM139385 United States
Howard Hughes Medical Institute (HHMI)Hanna H. Gray Fellowship United States
CitationJournal: Science / Year: 2021
Title: A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure.
Authors: Steve L Bonilla / Madeline E Sherlock / Andrea MacFadden / Jeffrey S Kieft /
Abstract: Viruses require multifunctional structured RNAs to hijack their host’s biochemistry, but their mechanisms can be obscured by the difficulty of solving conformationally dynamic RNA structures. Using ...Viruses require multifunctional structured RNAs to hijack their host’s biochemistry, but their mechanisms can be obscured by the difficulty of solving conformationally dynamic RNA structures. Using cryo–electron microscopy (cryo-EM), we visualized the structure of the mysterious viral transfer RNA (tRNA)–like structure (TLS) from the brome mosaic virus, which affects replication, translation, and genome encapsidation. Structures in isolation and those bound to tyrosyl-tRNA synthetase (TyrRS) show that this ~55-kilodalton purported tRNA mimic undergoes large conformational rearrangements to bind TyrRS in a form that differs substantially from that of tRNA. Our study reveals how viral RNAs can use a combination of static and dynamic RNA structures to bind host machinery through highly noncanonical interactions, and we highlight the utility of cryo-EM for visualizing small, conformationally dynamic structured RNAs.
History
DepositionSep 22, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0264
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0264
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7sam
  • Surface level: 0.0264
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_24952.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.41 Å/pix.
x 560 pix.
= 231.28 Å
0.41 Å/pix.
x 560 pix.
= 231.28 Å
0.41 Å/pix.
x 560 pix.
= 231.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.413 Å
Density
Contour LevelBy AUTHOR: 0.0264 / Movie #1: 0.0264
Minimum - Maximum-0.008608716 - 0.07794537
Average (Standard dev.)0.00013766829 (±0.0023975505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 231.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.4130.4130.413
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z231.280231.280231.280
α/β/γ90.00090.00090.000
start NX/NY/NZ-140-140-140
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-0.0090.0780.000

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Supplemental data

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Additional map: Sharpened (B factor: 257.7) cryo-EM map of brome...

Fileemd_24952_additional_1.map
AnnotationSharpened (B factor: 257.7) cryo-EM map of brome mosaic virus (BMV) tRNA-like structure (TLS) generated using cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half-map A of brome mosaic virus (BMV) t RNA-like...

Fileemd_24952_half_map_1.map
AnnotationHalf-map A of brome mosaic virus (BMV) tRNA-like structure (TLS) generated using cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half-map B of brome mosaic virus (BMV) t RNA-like...

Fileemd_24952_half_map_2.map
AnnotationHalf-map B of brome mosaic virus (BMV) tRNA-like structure (TLS) generated using cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire tRNA-like structure at the 3' UTR of the brome mosaic virus (BMV)...

EntireName: tRNA-like structure at the 3' UTR of the brome mosaic virus (BMV) genome
Details: RNA was generated by in vitro transcription of sequence-verified linear DNA template
Number of Components: 2

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Component #1: protein, tRNA-like structure at the 3' UTR of the brome mosaic vi...

ProteinName: tRNA-like structure at the 3' UTR of the brome mosaic virus (BMV) genome
Details: RNA was generated by in vitro transcription of sequence-verified linear DNA template
Recombinant expression: No
MassTheoretical: 54.56 kDa
SourceSpecies: Brome mosaic virus

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Component #2: nucleic-acid, Viral RNA

nucleic acidName: Viral RNARNA virus / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGCGUGGUUG ACACGCAGAC CUCUUACAAG AGUGUCUAGG UGCCUUUGAG AGUUACUCUU UGCUCUCUUC GGAAGAACCC UUAGGGGUUC GUGCAUGGGC UUGCAUAGCA AGUCUUAGAA UGCGGGUACC GUACAGUGUU GAAAAACACU GUAAAUCUCU AAAAGAGACC A
MassTheoretical: 55.044559 kDa
SourceSpecies: Brome mosaic virus

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionBuffer solution: Solution contained 10 mM magnesium chloride.
pH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 278 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 30 e/Å2 / Illumination Mode: OTHER
LensCs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: -2000.0 - -800.0 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 128226
3D reconstructionSoftware: cryoSPARC / Resolution: 4.3 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Output model

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