5FVC | pdb_00005fvc

Structure of RNA-bound decameric HMPV nucleoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.17 Å
  • R-Value Free: 
    0.230 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.191 (Depositor) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Nucleocapsid assembly in pneumoviruses is regulated by conformational switching of the N protein.

Renner, M.Bertinelli, M.Leyrat, C.Paesen, G.C.Saraiva de Oliveira, L.F.Huiskonen, J.T.Grimes, J.M.

(2016) Elife 5: e12627-e12627

  • DOI: https://doi.org/10.7554/eLife.12627
  • Primary Citation Related Structures: 
    5FVC, 5FVD

  • PubMed Abstract: 

    Non-segmented, (-)RNA viruses cause serious human diseases. Human metapneumovirus (HMPV), an emerging pathogen of this order of viruses (Mononegavirales) is one of the main causes of respiratory tract illness in children. To help elucidate the assembly mechanism of the nucleocapsid (the viral RNA genome packaged by the nucleoprotein N) we present crystallographic structures of HMPV N in its assembled RNA-bound state and in a monomeric state, bound to the polymerase cofactor P. Our structures reveal molecular details of how P inhibits the self-assembly of N and how N transitions between the RNA-free and RNA-bound conformational state. Notably, we observe a role for the C-terminal extension of N in directly preventing premature uptake of RNA by folding into the RNA-binding cleft. Our structures suggest a common mechanism of how the growth of the nucleocapsid is orchestrated, and highlight an interaction site representing an important target for antivirals.


  • Organizational Affiliation
    • Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 466.66 kDa 
  • Atom Count: 29,357 
  • Modeled Residue Count: 3,677 
  • Deposited Residue Count: 4,080 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HMPV NUCLEOPROTEIN
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
401human metapneumovirusMutation(s): 0 
UniProt
Find proteins for Q91F57 (human metapneumovirus)
Explore Q91F57 
Go to UniProtKB:  Q91F57
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91F57
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA70Escherichia coli BL21(DE3)
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.17 Å
  • R-Value Free:  0.230 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.191 (Depositor) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.01α = 90
b = 233.21β = 90
c = 203.64γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Database references
  • Version 1.2: 2017-03-22
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.4: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 1.5: 2024-05-01
    Changes: Data collection, Database references, Refinement description