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- EMDB-13476: NSP2 RNP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-13476
TitleNSP2 RNP complex
Map data
Sample
  • Complex: NSP2 RNP complex
    • Protein or peptide: Non-structural protein 2
KeywordsRNA Chaperone RNA folding Rotavirus / VIRAL PROTEIN
Function / homology
Function and homology information


nucleoside diphosphate kinase activity / viral genome replication / ribonucleoside triphosphate phosphatase activity / 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
Similarity search - Function
Rotavirus NSP2, N-terminal / Rotavirus NSP2, C-terminal / : / : / Rotavirus non-structural protein 35, C-terminal / Rotavirus non-structural protein 35, N-terminal / Rotavirus non-structural protein 2
Similarity search - Domain/homology
Non-structural protein 2
Similarity search - Component
Biological speciesRotavirus / Rotavirus A
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBravo JPK / Borodavka A
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust213437/Z/18/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011151/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Structural basis of rotavirus RNA chaperone displacement and RNA annealing.
Authors: Jack P K Bravo / Kira Bartnik / Luca Venditti / Julia Acker / Emma H Gail / Alice Colyer / Chen Davidovich / Don C Lamb / Roman Tuma / Antonio N Calabrese / Alexander Borodavka /
Abstract: Rotavirus genomes are distributed between 11 distinct RNA molecules, all of which must be selectively copackaged during virus assembly. This likely occurs through sequence-specific RNA interactions ...Rotavirus genomes are distributed between 11 distinct RNA molecules, all of which must be selectively copackaged during virus assembly. This likely occurs through sequence-specific RNA interactions facilitated by the RNA chaperone NSP2. Here, we report that NSP2 autoregulates its chaperone activity through its C-terminal region (CTR) that promotes RNA-RNA interactions by limiting its helix-unwinding activity. Unexpectedly, structural proteomics data revealed that the CTR does not directly interact with RNA, while accelerating RNA release from NSP2. Cryo-electron microscopy reconstructions of an NSP2-RNA complex reveal a highly conserved acidic patch on the CTR, which is poised toward the bound RNA. Virus replication was abrogated by charge-disrupting mutations within the acidic patch but completely restored by charge-preserving mutations. Mechanistic similarities between NSP2 and the unrelated bacterial RNA chaperone Hfq suggest that accelerating RNA dissociation while promoting intermolecular RNA interactions may be a widespread strategy of RNA chaperone recycling.
History
DepositionAug 26, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0205
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0205
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pkp
  • Surface level: 0.0205
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7pkp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13476.png

Downloads & links

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Map

FileDownload / File: emd_13476.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 220 pix.
= 235.4 Å		1.07 Å/pix.
x 220 pix.
= 235.4 Å		1.07 Å/pix.
x 220 pix.
= 235.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0205 / Movie #1: 0.0205
Minimum - Maximum-0.114697896 - 0.1695741
Average (Standard dev.)0.00028718478 (±0.005219577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 235.40001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z235.400235.400235.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.1150.1700.000

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Supplemental data

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Sample components

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Entire : NSP2 RNP complex

EntireName: NSP2 RNP complex
Components
  • Complex: NSP2 RNP complex
    • Protein or peptide: Non-structural protein 2

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Supramolecule #1: NSP2 RNP complex

SupramoleculeName: NSP2 RNP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rotavirus

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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: Rotavirus A
Molecular weightTheoretical: 36.23482 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAELACFCYP HLENDSYKFI PFNNLAIKAM LTAKVDKKDM DKFYDSIIYG IAPPPQFKKR YNTNDNSRGM NFETIMFTKV AMLICEALN SLKVTQANVS NVLSRVVSIR HLENLVIRKE NPQDILFHSK DLLLKSTLIA IGQSKEIETT ITAEGGEIVF Q NAAFTMWK ...String:
MAELACFCYP HLENDSYKFI PFNNLAIKAM LTAKVDKKDM DKFYDSIIYG IAPPPQFKKR YNTNDNSRGM NFETIMFTKV AMLICEALN SLKVTQANVS NVLSRVVSIR HLENLVIRKE NPQDILFHSK DLLLKSTLIA IGQSKEIETT ITAEGGEIVF Q NAAFTMWK LTYLEHQLMP ILDQNFIEYK VTLNEDKPIS DVHVKELVAE LRWQYNKFAV ITHGKGHYRI VKYSSVANHA DR VYATFKS NVKTGVNNDF NLLDQRIIWQ NWYAFTSSMK QGNTLDVCKR LLFQKMKPEK NPFKGLSTDR KMDEVS

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

BufferpH: 7.5
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: 55.0 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38252
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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