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- EMDB-47099: Structure of a Tick-Borne Flavivirus xrRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-47099
TitleStructure of a Tick-Borne Flavivirus xrRNA
Map data
Sample
  • Complex: Structure of a Tick-Borne Flavivirus xrRNA
    • RNA: RNA (440-MER)
  • Ligand: MAGNESIUM ION
KeywordsVirus / RNA / xrRNA / Exonuclease
Biological speciesPowassan virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLangeberg CJ / Kieft JS / Sherlock ME / Szucs MJ / Vicens Q
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI133348 United States
CitationJournal: Nat Commun / Year: 2025
Title: Tick-borne flavivirus exoribonuclease-resistant RNAs contain a double loop structure.
Authors: Conner J Langeberg / Matthew J Szucs / Madeline E Sherlock / Quentin Vicens / Jeffrey S Kieft /
Abstract: Viruses from the Flaviviridae family contain human relevant pathogens that generate subgenomic noncoding RNAs during infection using structured exoribonuclease resistant RNAs (xrRNAs). These xrRNAs ...Viruses from the Flaviviridae family contain human relevant pathogens that generate subgenomic noncoding RNAs during infection using structured exoribonuclease resistant RNAs (xrRNAs). These xrRNAs block progression of host cell's 5' to 3' exoribonucleases. The structures of several xrRNAs from mosquito-borne and insect-specific flaviviruses reveal a conserved fold in which a ring-like motif encircles the 5' end of the xrRNA. However, the xrRNAs found in tick-borne and no known vector flaviviruses have distinct characteristics, and their 3-D fold was unsolved. Here, we verify the presence of xrRNAs in the encephalitis-causing tick-borne Powassan Virus. We characterize their secondary structure and obtain a mid-resolution map of one of these xrRNAs using cryo-EM, revealing a unique double-loop ring element. Integrating these results with covariation analysis, biochemical data, and existing high-resolution structural information yields a model in which the core of the fold matches the previously solved xrRNA fold, but the expanded double loop ring is remodeled upon encountering the exoribonuclease. These results are representative of a broad class of xrRNAs and reveal a conserved strategy of structure-based exoribonuclease resistance achieved through a unique topology across a viral family of importance to global health.
History
DepositionSep 20, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47099.png

Downloads & links

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Map

FileDownload / File: emd_47099.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 512 pix.
= 403.456 Å		0.79 Å/pix.
x 512 pix.
= 403.456 Å		0.79 Å/pix.
x 512 pix.
= 403.456 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.06245186 - 0.34797153
Average (Standard dev.)0.00009042955 (±0.0070658536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 403.456 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47099_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47099_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of a Tick-Borne Flavivirus xrRNA

EntireName: Structure of a Tick-Borne Flavivirus xrRNA
Components
  • Complex: Structure of a Tick-Borne Flavivirus xrRNA
    • RNA: RNA (440-MER)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Structure of a Tick-Borne Flavivirus xrRNA

SupramoleculeName: Structure of a Tick-Borne Flavivirus xrRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Powassan virus
Molecular weightTheoretical: 142.44 KDa

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Macromolecule #1: RNA (440-MER)

MacromoleculeName: RNA (440-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Powassan virus
Molecular weightTheoretical: 142.224047 KDa
SequenceString: UAGGGGGUGA UGUGGCAGCG CACUUGAUAU GGAUGCAGUU CACAGACUAA AUGUCGGUCG GGGAAGAUGU AUUCUUCUCA UAAGAUAUA GUCGGACCUC UCCUUAAUGG GAGCUAGCGG AUGAAGUGAU GCAACACUGG AGCCGCUGGG AACUAAUUUG U AUGCGAAA ...String:
UAGGGGGUGA UGUGGCAGCG CACUUGAUAU GGAUGCAGUU CACAGACUAA AUGUCGGUCG GGGAAGAUGU AUUCUUCUCA UAAGAUAUA GUCGGACCUC UCCUUAAUGG GAGCUAGCGG AUGAAGUGAU GCAACACUGG AGCCGCUGGG AACUAAUUUG U AUGCGAAA GUAUAUUGAU UAGUUUUGGA GAAAGUUAUC AGGCAUGCAC CUGGUAGCUA GUCUUUAAAC CAAUAGAUUG CA UCGGUUU AAAAGGCAAG ACCGUCAAAU UGCGGGAAAG GGGUCAACAG CCGUUCAGUA CCAAGUCUCA GGGGAAACUU UGA GAUGGC CUUGCAAAGG GUAUGGUAAU AAGCUGACGG ACAUGGUCCU AACCACGCAG CCAAGUCCUA AGUCAAGUGA CGGG AAAAG GUCGUCCCCG ACGCAUCAUC CCUCUAUGCG AGACC

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 19 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration3.0 mg/mL
BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 12 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1061023
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 55485
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 65000 / Software - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7k16

source_name: PDB, initial_model_type: experimental model

8tjx

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 150.22
Output model

PDB-9dp9:
Structure of a Tick-Borne Flavivirus xrRNA

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