5N2U | pdb_00005n2u

Influenza D virus nucleoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.252 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.202 (Depositor) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

The structure of the nucleoprotein of Influenza D shows that all Orthomyxoviridae nucleoproteins have a similar NPCORE, with or without a NPTAILfor nuclear transport.

Donchet, A.Oliva, J.Labaronne, A.Tengo, L.Miloudi, M.C A Gerard, F.Mas, C.Schoehn, G.W H Ruigrok, R.Ducatez, M.Crepin, T.

(2019) Sci Rep 9: 600-600

  • DOI: https://doi.org/10.1038/s41598-018-37306-y
  • Primary Citation Related Structures: 
    5N2U

  • PubMed Abstract: 

    This paper focuses on the nucleoprotein (NP) of the newly identified member of the Orthomyxoviridae family, Influenza D virus. To date several X-ray structures of NP of Influenza A (A/NP) and B (B/NP) viruses and of infectious salmon anemia (ISA/NP) virus have been solved. Here we purified, characterized and solved the X-ray structure of the tetrameric D/NP at 2.4 Å resolution. The crystal structure of its core is similar to NP of other Influenza viruses. However, unlike A/NP and B/NP which possess a flexible amino-terminal tail containing nuclear localization signals (NLS) for their nuclear import, D/NP possesses a carboxy-terminal tail (D/NP TAIL ). We show that D/NP TAIL harbors a bipartite NLS and designed C-terminal truncated mutants to demonstrate the role of D/NP TAIL for nuclear transport.


  • Organizational Affiliation
    • Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 245.56 kDa 
  • Atom Count: 14,881 
  • Modeled Residue Count: 1,872 
  • Deposited Residue Count: 2,208 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoprotein
A, B, C, D
552Influenza D virus (D/bovine/France/2986/2012)Mutation(s): 0 
Gene Names: NP
UniProt
Find proteins for A0A0E3VZU8 (Influenza D virus)
Explore A0A0E3VZU8 
Go to UniProtKB:  A0A0E3VZU8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E3VZU8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.252 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.202 (Depositor) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.166α = 91.2
b = 85.166β = 101.94
c = 103.385γ = 101.02
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-14-CE09-0017
French National Research AgencyFranceANR-10-LABX-49-01

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description