5OIY | pdb_00005oiy

Structure of the HMPV P oligomerization domain at 2.2 A

• PDB DOI: https://doi.org/10.2210/pdb5OIY/pdb

• Classification: VIRAL PROTEIN
• Organism(s): human metapneumovirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-19 Released: 2017-11-15 
• Deposition Author(s): Renner, M., Paesen, G.C., Grison, C.M., Granier, S., Grimes, J.M., Leyrat, C.
• Funding Organization(s): Wellcome Trust, European Union, Medical Research Council (United Kingdom), Labex EpiGenMed

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.265 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.249 (DCC) 

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

• PubMed: 29093501 
• DOI: https://doi.org/10.1038/s41598-017-14448-z
• Primary Citation 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.

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Organizational Affiliation: 
• Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford, OX3 7BN, UK.
Institut de Génomique Fonctionnelle, CNRS UMR-5203 INSERM U1191, University of Montpellier, Montpellier, France.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford, OX3 7BN, UK. [e-mail].
Science Division, Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom. [e-mail].
Institut de Génomique Fonctionnelle, CNRS UMR-5203 INSERM U1191, University of Montpellier, Montpellier, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 106.06 kDa 
• Atom Count: 1,653 
• Modeled Residue Count: 203 
• Deposited Residue Count: 944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoprotein	A, B, C, D, E, F, G, H	118	human metapneumovirus	Mutation(s): 0
UniProt
Find proteins for Q91KZ5 (human metapneumovirus) Explore Q91KZ5  Go to UniProtKB:  Q91KZ5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.265 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.249 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.847	α = 90
b = 45.437	β = 90
c = 116.808	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Renner, M., Paesen, G.C., Grison, C.M., Granier, S., Grimes, J.M., Leyrat, C.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	204703/Z/16/Z
European Union	United Kingdom	FP7/2007-2013
Medical Research Council (United Kingdom)	United Kingdom	MR/L017709/1
Labex EpiGenMed	France	ANR-10-LABX-12-01

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.2: 2019-07-10
  Changes: Data collection
• Version 1.3: 2019-10-16
  Changes: Data collection
• Version 1.4: 2024-05-08
  Changes: Advisory, Data collection, Database references