5OIX

Structure of the HMPV P oligomerization domain at 1.6 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural dissection of human metapneumovirus phosphoprotein using small angle x-ray scattering.

Renner, M.Paesen, G.C.Grison, C.M.Granier, S.Grimes, J.M.Leyrat, C.

(2017) Sci Rep 7: 14865-14865

  • DOI: https://doi.org/10.1038/s41598-017-14448-z
  • Primary Citation of Related Structures:  
    5OIX, 5OIY

  • PubMed Abstract: 

    The phosphoprotein (P) is the main and essential cofactor of the RNA polymerase (L) of non-segmented, negative-strand RNA viruses. P positions the viral polymerase onto its nucleoprotein-RNA template and acts as a chaperone of the nucleoprotein (N), thereby preventing nonspecific encapsidation of cellular RNAs. The phosphoprotein of human metapneumovirus (HMPV) forms homotetramers composed of a stable oligomerization domain (P core ) flanked by large intrinsically disordered regions (IDRs). Here we combined x-ray crystallography of P core with small angle x-ray scattering (SAXS)-based ensemble modeling of the full-length P protein and several of its fragments to provide a structural description of P that captures its dynamic character, and highlights the presence of varyingly stable structural elements within the IDRs. We discuss the implications of the structural properties of HMPV P for the assembly and functioning of the viral transcription/replication machinery.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford, OX3 7BN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoprotein
A, B, C, D, E
A, B, C, D, E, F, G, H
118human 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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29α = 90
b = 110.44β = 95.62
c = 38.73γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom204703/Z/16/Z
European UnionUnited KingdomFP7/2007-2013
Medical Research Council (United Kingdom)United KingdomMR/L017709/1
Labex EpiGenMedFranceANR-10-LABX-12-01

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection