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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13476 | |||||||||
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Title | NSP2 RNP complex | |||||||||
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![]() | RNA Chaperone RNA folding Rotavirus / VIRAL PROTEIN | |||||||||
Function / homology | ![]() nucleoside diphosphate kinase activity / ribonucleoside triphosphate phosphatase activity / 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 Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Bravo JPK / Borodavka A | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.5 KB 9.5 KB | Display Display | ![]() |
Images | ![]() | 112.3 KB | ||
Filedesc metadata | ![]() | 5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pkpMC ![]() 7pkoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : NSP2 RNP complex
Entire | Name: NSP2 RNP complex |
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Components |
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-Supramolecule #1: NSP2 RNP complex
Supramolecule | Name: NSP2 RNP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Non-structural protein 2
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 36.23482 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38252 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |