+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13474 | |||||||||
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Title | CryoEM structure of Rotavirus NSP2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA chaperone Rotavirus RNA folding / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information 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 | Rotavirus / Rotavirus A | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Bravo JPK / Borodavka A | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13474.map.gz | 4.8 MB | EMDB map data format | |
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Header (meta data) | emd-13474-v30.xml emd-13474.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | emd_13474.png | 111.4 KB | ||
Filedesc metadata | emd-13474.cif.gz | 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13474 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13474 | HTTPS FTP |
-Validation report
Summary document | emd_13474_validation.pdf.gz | 407.5 KB | Display | EMDB validaton report |
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Full document | emd_13474_full_validation.pdf.gz | 407.1 KB | Display | |
Data in XML | emd_13474_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | emd_13474_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13474 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13474 | HTTPS FTP |
-Related structure data
Related structure data | 7pkoMC 7pkpC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13474.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Rotavirus NSP2 RNP complex
Entire | Name: Rotavirus NSP2 RNP complex |
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Components |
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-Supramolecule #1: Rotavirus NSP2 RNP complex
Supramolecule | Name: Rotavirus NSP2 RNP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Rotavirus |
-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: Rotavirus A |
Molecular weight | Theoretical: 36.23482 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 110.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109391 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |