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- PDB-7pkp: NSP2 RNP complex -

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Basic information

Entry
Database: PDB / ID: 7pkp
TitleNSP2 RNP complex
ComponentsNon-structural protein 2
KeywordsVIRAL PROTEIN / RNA Chaperone RNA folding Rotavirus
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 A
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBravo, J.P.K. / Borodavka, A.
Funding support United Kingdom, 2items
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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.0Sep 29, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 29, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 29, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Sep 29, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 29, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Sep 29, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 29, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.3Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
U: Non-structural protein 2
A: Non-structural protein 2
B: Non-structural protein 2
C: Non-structural protein 2
D: Non-structural protein 2
E: Non-structural protein 2
F: Non-structural protein 2
G: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)289,8798
Polymers289,8798
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area19180 Å2
ΔGint-98 kcal/mol
Surface area120170 Å2
MethodPISA

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Components

#1: Protein
Non-structural protein 2 / NSP2 / NCVP3 / Non-structural RNA-binding protein 35 / NS35


Mass: 36234.820 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Gene: NSP2 / Production host: Escherichia coli (E. coli)
References: UniProt: A2T3N6, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NSP2 RNP complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Rotavirus
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38252 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00820792
ELECTRON MICROSCOPYf_angle_d0.6828072
ELECTRON MICROSCOPYf_dihedral_angle_d5.04512640
ELECTRON MICROSCOPYf_chiral_restr0.0433136
ELECTRON MICROSCOPYf_plane_restr0.0043552

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