5FVD | pdb_00005fvd

Human metapneumovirus N0-P complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.205 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5FVD

This is version 1.3 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: 97.96 kDa 
  • Atom Count: 6,295 
  • Modeled Residue Count: 739 
  • Deposited Residue Count: 882 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NUCLEOCAPSID
A, C
394human 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 proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOSPHOPROTEIN
B, D
47human metapneumovirusMutation(s): 0 
UniProt
Find proteins for Q91KZ5 (human metapneumovirus)
Explore Q91KZ5 
Go to UniProtKB:  Q91KZ5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91KZ5
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.205 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.93α = 90.97
b = 62.78β = 96.38
c = 86.71γ = 108.98
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description