3BBZ

Structure of the nucleocapsid-binding domain from the mumps virus phosphoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the nucleocapsid-binding domain from the mumps virus polymerase; an example of protein folding induced by crystallization

Kingston, R.L.Gay, L.S.Baase, W.S.Matthews, B.W.

(2008) J.Mol.Biol. 379: 719-731

  • DOI: 10.1016/j.jmb.2007.12.080

  • PubMed Abstract: 
  • The human pathogen mumps virus, like all paramyxoviruses, encodes a polymerase responsible for virally directed RNA synthesis. The template for the polymerase is the nucleocapsid, a filamentous protein-RNA complex harboring the viral genome. Interact ...

    The human pathogen mumps virus, like all paramyxoviruses, encodes a polymerase responsible for virally directed RNA synthesis. The template for the polymerase is the nucleocapsid, a filamentous protein-RNA complex harboring the viral genome. Interaction of the polymerase and the nucleocapsid is mediated by a small domain tethered to the end of the phosphoprotein (P), one of the polymerase subunits. We report the X-ray crystal structure of this region of mumps virus P (the nucleocapsid-binding domain, or NBD, amino acids 343-391). The mumps P NBD forms a compact bundle of three alpha-helices within the crystal, a fold apparently conserved across the Paramyxovirinae. In solution, however, the domain exists in the molten globule state. This is demonstrated through application of differential scanning calorimetry, circular dichroism spectroscopy, NMR spectroscopy, and dynamic light scattering. While the mumps P NBD is compact and has persistent secondary structure, it lacks a well-defined tertiary structure under normal solution conditions. It can, however, be induced to fold by addition of a stabilizing methylamine cosolute. The domain provides a rare example of a molten globule that can be crystallized. The structure that is stabilized in the crystal represents the fully folded state of the domain, which must be transiently realized during binding to the viral nucleocapsid. While the intermolecular forces that govern the polymerase-nucleocapsid interaction appear to be different in measles, mumps, and Sendai viruses, for each of these viruses, polymerase translocation involves the coupled binding and folding of protein domains. In all cases, we suggest that this will result in a weak-affinity protein complex with a short lifetime, which allows the polymerase to take rapid steps forward.


    Organizational Affiliation

    School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. rl.kingston@auckland.ac.nz




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P protein
A, B
49Mumps virus (strain Jeryl-Lynn)Mutation(s): 1 
Gene Names: P
Find proteins for Q9J4L6 (Mumps virus (strain Jeryl-Lynn))
Go to UniProtKB:  Q9J4L6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download SDF File 
Download CCD File 
A, B
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 23.992α = 90.00
b = 55.485β = 90.00
c = 60.019γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
MLPHAREphasing
REFMACrefinement
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance