4LP7

Crystal structure of the human metapneumovirus matrix protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and self-assembly of the calcium binding matrix protein of human metapneumovirus.

Leyrat, C.Renner, M.Harlos, K.Huiskonen, J.T.Grimes, J.M.

(2014) Structure 22: 136-148

  • DOI: https://doi.org/10.1016/j.str.2013.10.013
  • Primary Citation of Related Structures:  
    4LP7

  • PubMed Abstract: 

    The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus M at 2.8 Å resolution in its native dimeric state. The structure reveals the presence of a high-affinity Ca²⁺ binding site. Molecular dynamics simulations (MDS) predict a secondary lower-affinity site that correlates well with data from fluorescence-based thermal shift assays. By combining small-angle X-ray scattering with MDS and ensemble analysis, we captured the structure and dynamics of M in solution. Our analysis reveals a large positively charged patch on the protein surface that is involved in membrane interaction. Structural analysis of DOPC-induced polymerization of M into helical filaments using electron microscopy leads to a model of M self-assembly. The conservation of the Ca²⁺ binding sites suggests a role for calcium in the replication and morphogenesis of pneumoviruses.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix protein M
A, B, C, D
254human metapneumovirusMutation(s): 0 
Gene Names: M
UniProt
Find proteins for Q91F56 (Human metapneumovirus)
Explore Q91F56 
Go to UniProtKB:  Q91F56
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91F56
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.009α = 90
b = 62.009β = 90
c = 275.385γ = 120
Software Package:
Software NamePurpose
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
GDAdata collection
HKL-2000data reduction
SCALAdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-01-29
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description