8P00 | pdb_00008p00

Cryo-EM structure of Rotavirus B NSP2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Cryo-EM structure of rotavirus B NSP2 reveals its unique tertiary architecture.

Chamera, S.Wycisk, K.Czarnocki-Cieciura, M.Nowotny, M.

(2024) J Virol 98: e0166023-e0166023

  • DOI: https://doi.org/10.1128/jvi.01660-23
  • Primary Citation Related Structures: 
    8P00

  • PubMed 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 in silico 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.


  • Organizational Affiliation
    • Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.

Macromolecule Content 

  • Total Structure Weight: 276.61 kDa 
  • Atom Count: 16,992 
  • Modeled Residue Count: 2,376 
  • Deposited Residue Count: 2,408 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-structural protein 2
A, B, C, D, E
A, B, C, D, E, F, G, H
301Human rotavirus B strain CAL-1Mutation(s): 0 
Gene Names: NSP2
EC: 3.6.4
UniProt
Find proteins for Q9J3T3 (Human rotavirus B strain CAL-1)
Explore Q9J3T3 
Go to UniProtKB:  Q9J3T3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9J3T3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Source and taxonomy