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- EMDB-17323: Cryo-EM structure of Rotavirus B NSP2 -

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Basic information

Entry
Database: EMDB / ID: EMD-17323
TitleCryo-EM structure of Rotavirus B NSP2
Map data
Sample
  • Complex: Homooctamer of NSP2
    • Protein or peptide: Non-structural protein 2
KeywordsOctamer / RNA binding / Rotavirus / RNA chaperone / VIRAL PROTEIN
Function / homologyhydrolase activity, acting on acid anhydrides / Rotavirus non-structural protein 2 / viral genome replication / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / RNA binding / ATP binding / metal ion binding / Non-structural protein 2
Function and homology information
Biological speciesRotavirus B / Human rotavirus B strain CAL-1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChamera S / Nowotny M
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: J Virol / Year: 2024
Title: Cryo-EM structure of rotavirus B NSP2 reveals its unique tertiary architecture.
Authors: Sebastian Chamera / Krzysztof Wycisk / Mariusz Czarnocki-Cieciura / Marcin Nowotny /
Abstract: Rotavirus (RV) NSP2 is a multifunctional RNA chaperone that exhibits numerous activities that are essential for replication and viral genome packaging. We performed an analysis that highlighted a ...Rotavirus (RV) NSP2 is a multifunctional RNA chaperone that exhibits numerous activities that are essential for replication and viral genome packaging. We performed an analysis that highlighted a distant relationship of NSP2 from rotavirus B (RVB) to proteins from other human RVs. We solved a cryo-electron microscopy structure of RVB NSP2 that shows structural differences with corresponding proteins from other human RVs. Based on the structure, we identified amino acid residues that are involved in RNA interactions. Anisotropy titration experiments showed that these residues are important for nucleic acid binding. We also identified structural motifs that are conserved in all RV species. Collectively, our data complete the structural characterization of rotaviral NSP2 protein and demonstrate its structural diversity among RV species.IMPORTANCERotavirus B (RVB), also known as adult diarrhea rotavirus, has caused epidemics of severe diarrhea in China, India, and Bangladesh. Thousands of people are infected in a single RVB epidemic. However, information on this group of rotaviruses remains limited. As NSP2 is an essential protein in the viral life cycle, including its role in the formation of replication factories, it may be a target for future antiviral strategy against viruses with similar mechanisms.
History
DepositionMay 9, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17323.png

Downloads & links

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Map

FileDownload / File: emd_17323.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.301
Minimum - Maximum-0.8284862 - 1.7407005
Average (Standard dev.)0.00381548 (±0.05772422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 240.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_17323_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: #1

Fileemd_17323_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 : Homooctamer of NSP2

EntireName: Homooctamer of NSP2
Components
  • Complex: Homooctamer of NSP2
    • Protein or peptide: Non-structural protein 2

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Supramolecule #1: Homooctamer of NSP2

SupramoleculeName: Homooctamer of NSP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rotavirus B / Strain: Mexico

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Macromolecule #1: Non-structural protein 2

MacromoleculeName: Non-structural protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Human rotavirus B strain CAL-1
Molecular weightTheoretical: 34.575672 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTQSVSLSDF IVKTEDGYMP SDRECVALDR YLSKEQKELR ETFKDGKNDR SALRIKMFLS PSPSRRFTQH GVVPMREIKT NTDIPSTLW TLVTDWLLNL LQDEENQEMF EDFISSKFPD VLASADKLAR FAQRLEDRKD VLHKNFSKAM NAFGACFWAI K PTFATEGK ...String:
MTQSVSLSDF IVKTEDGYMP SDRECVALDR YLSKEQKELR ETFKDGKNDR SALRIKMFLS PSPSRRFTQH GVVPMREIKT NTDIPSTLW TLVTDWLLNL LQDEENQEMF EDFISSKFPD VLASADKLAR FAQRLEDRKD VLHKNFSKAM NAFGACFWAI K PTFATEGK CNVVRATDDS MILEFQPVPE YFRCGRSKAT FYKLYPLSDE QPVNGMLALK AVAGNQFFMY HGHGHIRTVP YH ELADAIK SYARKDKETL ESISKSPLAA QCGSKFLDML DGIRSKQKIE DVILKAKIFE KKRS

UniProtKB: Non-structural protein 2

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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

Concentration0.36 mg/mL
BufferpH: 7
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.92 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22131

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